Saruman's Uruk-hai - having captured Merry and Pippin - are supposed to be running back to Isengard, but as the camera pans downwards to show them for the first time, it's clear that they are just walking and only start to run as the camera points directly at them.
When the Rohirrim surround Aragorn, Legolas and Gimli at the beginning, you can see Éomer's lips moving in one of the wider shots and he obviously talks to the three but there is no sound coming out of his mouth.
During the battle of Helm's Deep, Aragorn orders the archers to shoot by yelling 'Fire!'. This command appeared after the introduction of firearms. Earlier, an archer commander would use the command 'Shoot!' or 'Release!'.
In the extended edition, in the stable at Edoras, Aragorn tells the stable hands to set the horse Brego free. When the horse Brego comes to Aragorn at the riverbank, he is wearing a halter and rope. A good horseman would never leave a halter on a horse when he is loosed into the wild, as it could get hung up on a branch or other obstacle and cause the horse injury. Likewise they would not leave a lead rope dangling off a halter even if turning the horse into a pasture. The lead is so long that it drags between the horse's legs; this would be a hazard.
When freeing Pippin and Merry from the roots of the tree that has engulfed them, one of the things Treebeard tells the tree is to go away and 'eat earth'. While trees do take some nutrients from the ground, this amount is negligible, the overwhelming mass of a tree comes from the carbon dioxide absorbed by the tree's leaves. It is a common misconception (that trees get a significant amount of, if not all, their mass from the earth), and being an Ent or Tree-herder, Treebeard should know this.
Legolas' eyes are brown for the majority of the battle of Helm's Deep, instead of their customary blue. However, it is reported that this particular color change came about when Orlando Bloom's blue contact lenses were forgotten during some of the shooting for this sequence.
Pippin's hands are tied, but when he falls under the horse, his hands are untied and apart. When Aragorn is working out what happened we see, in the flashbacks, that Pippin did not cut his bonds until after the horse incident.
When Gandalf the White first enters Theoden's hall, the position of his staff changes from being held perpendicular to the ground to being held parallel between shots. Director Peter Jackson noticed this error for the first time while recording the Director's Commentary for the Extended Edition of the DVD.
In the storeroom where Sam is suggesting that Frodo use the Ring to escape, Frodo is initially sitting in front of a barrel. When Faramir arrives, Frodo and Sam are sitting on a cloak and there are no barrels in sight.
While on their way to Helm's Deep, Gimli is telling tales to Eowin and Aragorn in order to while away the long hours of the trip. At several points, however, you can see the direction of the battle ax's head change from blade forward to blade backwards then forwards again, all within mere seconds of each other.
When Merry and Pippin are dropped to the ground by the Uruk-Hai, Merry is lying very close to Pippin. In the next shot Pippin is obviously a few feet away for he has to crawl closer to Merry to be able to talk to him
When King Theoden is having his armor strapped on, his aide fastens the left shoulder strap, then we see the leg greaves being strapped on, and gloves being tied. In the next shot, the aide goes to fasten the left shoulder strap again, and there are no greaves on his legs or gloves on his hands.
When Legolas shoots the rope of one of the big ladders, the previous shot has already shown the ladder to be past straight vertical position. The ladder should continue it's arc towards the wall, but instead it falls back.
After Legolas shoots two arrows into the shoulder region of the Uruk-Hai running with the torch, the arrows are nowhere to be seen in the shot that shows the runner diving into drain on the side of the wall of Helms Deep.
When the men of Rohan are in Helm's Deep preparing for war against the orcs of Isengard, we see Aragorn calls a young boy over to see his sword. After which telling him, "this is a good sword", he brings the sword closer in to his body. But instead of the sword appearing in front of him, it appears behind him.
When Frodo and Sam are hidden under the elvish cloak at the Black Gate, we can see from under the cape the feet of the enemy soldier through a gap in between the cloth and the floor. But in the next shoot when Frodo unfold the cape (that looks like a rock) we can see it was well buried in the dust and there is no possible gap.
While everyone was amazed by Legolas' skill in firing three arrows in quick succession whilst sliding down the stairs on an Uruk-shield, you can clearly see that each shot is cut when he is about half way down the stairs, i.e. he only had time to fire one arrow.
When Frodo, Sam, and Gollum are in the Dead Marsh and the Nazgul flies over, Frodo goes after the ring with his left hand, which Sam grabs and holds. Frodo is then shown putting his right hand to his chest, but in the wide shot, his right hand is still lying at his side.
In the scene where Treebeard the ent is carrying Merry and Pippen through the forest explaining to them about the lack of Ent-wives, the location of the branches around his head keep moving. Either they are from the side of his head and his shoulder, two out of his head, or none at all.
When Legolas is pulling Gimli and Aragorn to safety using the rope during the battle of Helm's Deep, Gimli is on Aragorn's right side for every shot except the first close-up of Aragorn in Gimli, where he is clearly on Aragorn's left.
In Helms Deep, as Legolas throws the shield onto the stairs, he has his bow in his left hand. As he runs to jump onto the shield, the bow is gone. As he is sliding down the stairs, he is using the bow again.
When Gandalf and Theoden are talking outside town, near the burial mounds covered in white flowers, all the shots of Gandalf show the wind whipping his hair around, but in all the shots of Theoden there is not even a hint of a breeze in his hair.
When the three ladders are raised on the Keep in the Helms Deep sequence, the wide and close-in shots alternate between the outer two ladders being about 30 feet apart and less than 5 feet apart, respectively (the third is in between them and never makes it up).
When the orcs are carrying Merry and Pippin on their backs the wide shots show the orc carrying Pippin to be closer to the camera with the orc carrying Merry to his left. But in the close-ups they have swapped places with Pippin having to turn to his right to speak to Merry.
When Éomer and company ambush the Uruk-hai, we see Pippin as he is almost trampled by a horse. When the shot cuts to Pippin, his arms are unbound and free as he moves to defend himself. When he rolls away, however, his hands are bound.
At the beginning of the battle at Helm's Deep, the people in the fortress are seen drawing their arrows before one of them is accidentally released. Soon, they are seen drawing their arrows again, despite the fact that they should have still been drawn from the first time.
In the very first scene of the movie, the flashback from The Fellowship of the Ring, when Gandalf has his confrontation with the Balrog, Frodo yells "NO" before Gandalf falls, but in FOTR, Gandalf falls and then Frodo yells "NO".
Near the end of the battle for Helm's Deep, Theoden, Aragorn and others are waiting for the Orcs to break through the door. In the next shot they are on horses charging toward the Orcs. There were no horses around to begin with.
When Aragorn, Legolas and Gimli are first introduced to Gandalf the White in Fangorn forest, Gandalf replies "yes, Gandalf, that is what they used to call me, Gandalf the Grey" when Aragron mentions his name. In reality, Gandalf would already be aware of his name as Treebeard had previously delivered the Hobbits Merry and Pippin to him, who would have obviously called him Gandalf when they met him.
When Aragorn, Gimli, Legolas, and Gandalf first enter the Golden Hall of Edoras, Legolas is supporting Gandalf with his arm. When the door is shut behind them he lets go and in the next shot their arms are together again.
Very near the beginning of the Extended version, some of the real fog in a valley visible at a distance behind Frodo and Sam abruptly disappears. While some close-ups were filmed in studio, it is also possible that there was a delay in filming these "on location" shots.
In the dream sequence with Aragorn and Arwen, after Arwen says "Then, it is a good dream," there is one shot where her hair covers both ears completely. All the rest of the shots have both ears plainly visible.
When Aragorn mounts the horse Brego at the river, the horse's lead rope is dangling from the halter. It looks very clean, not like a lead that has been dragged on the ground for days or weeks. Though Aragorn is weak, he is evidently able to reach forward and tie the loose end of the rope back to the halter to make reins. Later, after he sees the Orc army approaching and gallops toward Helm's Deep, you can see that Brego's mouth is lathered, and when they stop on the hilltop it's very clear that there is a bit in his mouth. Where did that come from?
When Sméagol/Gollum have a discussion while the Hobbits are asleep, he can be seen from one angle as Sméagol and from the other angle as Gollum. When Sméagol puts his hands above his ears, Gollum does not have his hands up to his ears. Since the state of Sméagol/Gollum is psychological, this could not happen, as can later be seen when Sméagol/Gollum is questioned by the Gondorians.
While Aragorn, Legolas, and Gimli are tracking the Uruk-hai, Aragorn asks "Legolas, what do your elf eyes see?" And Legolas responds, "The Uruks turn northeast, they're taking the hobbits to Isengard!" If the Uruks turned northeast, they would be traveling away from Isengard, since Isengard is northwest of their location.
During the battle of Helm's Deep, after the wall has been breached and Haldir dies, Aragorn gets on an Uruk-Hai ladder and drops himself into the advancing Uruk-Hai. In the wide shot it can be clearly seen that the ladder has been raised against the Deeping Wall from inside the castle. When, how and why did the Uruks raise a ladder there, when two flights of stairs are already available?
When the gate to Mordor is opened, it is clearly seen to be as thick as the wall, and each corner is seen to be a right angle. There is no space at all in between the gate and the wall when it is closed, later on in the same scene. However, the gate opens on a curve, and so would get stuck every time it opened or closed, unless the wall was somehow retracted. We do not see the wall retracted at all, thus it is physically impossible for such a gate to exist.
During the battle with the Warg riders, a Warg and Orc fall across Gimli. Visibly struggling to lift them off, there is no change in effort or position when a second Warg puts its weight on Gimli. This should be an addition of several hundred pounds.
In the extended DVD edition, Dominic Monaghan points out in the cast commentary that in one of the aerial shots of the Uruk-Hai taking the Hobbits to Isengard, Merry and Pippin are nowhere to be seen. This is false. Both Hobbits are wearing green capes which can be easily made out without freeze-framing the scene. The Hobbits are being carried by two Uruks in the third line from the front of the group. (Extended Edition DVD Time Code: Disc 1, 26m20s)
When Shadowfax first appears, there are tracks across the paddock behind and to the right of him. Some say these are tire tracks, others argue that they could just as easily be the wheel ruts of a farm cart. In response, the first group say that the ruts are too far apart to be from a farm cart, and the space in between is too narrow, meaning that they are definitely those of a car or truck.
When Faramir's party is called back to Osgiliath, they stop on a ridge looking toward the city. In the distance, you can see Minas Tirith, which is west of Osgiliath; therefore the party is on the eastern side of the Anduin. Once they reach the city, one of the men of Gondor mentions that Mordor's forces have taken the eastern half of the city. So how did Faramir's party get to the western side? If they used the sewer that Faramir sends Frodo and Sam into later, why did he have to explain to them what those sewers were at that time? They'd already have been through them once.
When the Westfold village is being attacked by the Hill Folk there seems to be only one horse in the village; as these are the people of Rohan ("The Horse Lands") we can assume the fighting men & their horses are away but where are the rest of the horses? There should be mares, foals, yearlings, & older horses no longer fit for fighting quite near to the village (there is a corral clearly visible in the village).
In Fangorn forest, Gandalf tells Aragorn that Sauron fears him, fears what he may become. But Aragorn had spent his entire life hiding from Sauron, even concealing his own identity to stay safe and hidden from Sauron. In the books he only reveals himself to Sauron by using Saruman's palantír to wrestle with Sauron, and that only the night before he sets off through the Paths of the Dead. This deviation in the film creates a major plot hole. If Aragorn has been hidden all his life, and never revealed himself in the Orthanc stone, then how can Sauron know of his existence? There's nobody who could have told him, because the only one who might have was Saruman, who wanted the Ring for himself. And more, if Sauron had somehow managed to find out so soon that Aragorn was the living heir of Isildur, he would have had no choice but to launch his planned assault on Gondor immediately, which would have caught the men of the West off guard long before they were prepared. The Rohirrim could not have come to their aid, and Aragorn had not yet called the Dead to honour their oath. Gondor would have stood alone, Minas Tirith would have been sacked, and so first Gondor and then Rohan would have fallen. Sauron would not have been distracted by Gondor's army at the Black Gates, Frodo would inevitably have been caught and the Ring returned to its Master. And so Middle Earth would have fallen into a new Age of Darkness.
The face-off between Frodo and the winged Nazgûl is a serious plot hole in the film. The whole point of the quest of the Fellowship was to leave Sauron in doubt about the whereabouts of the Ring, and to distract him from it and its location as it is carried closer to Mordor. That was the only chance for the quest to succeed. As far as he knows the Ring is missing somewhere in the region of the Shire, and nothing leads him to believe otherwise. But putting Frodo directly in front of a Nazgûl in Osgiliath, about to put the Ring on, would alert Sauron to the fact that the Ring not only has been found, but it's in Gondor and is perilously close to his borders. He would have immediately thrown the full weight of all his armies on Gondor to reclaim the Ring and the war would have been lost.
The Ents refusing to fight in the war is a major plot hole. It ignores the fact that the Ents knew everything that happened within the borders of Fangorn, and that they knew of the orcs' destruction of the southern borders of the forest long before the hobbits had even arrived.
The sub plot of Faramir taking the hobbits to Osgiliath reduces him to no better than his brother. The entire reason for the contrast between the brothers was to show that Faramir was the better man who did not give into the Ring's temptation, least of all for the very petty chance of sucking up to his father. If he had been as weak as Boromir, Aragorn would not have been so quick to make him his Steward when he took the throne.
In Helms Deep, when people are moving deeper into the caves (as orcs are storming the keep), we see a woman put her hand on one of the stalactites as she passes it. When she releases it it sways gently.
When Theodred is carried to the graveyard, his heavy scale mail armor is caught in the wind; a heavy looking item supposedly made from steel plates with tough leather on the backside, but none the less it flaps in the wind.
(Flipped shot) When Legolas says in Elvish, "There's something out there," the Elvish Brooches (leaf brooches holding their cloaks together) are facing the opposite direction. Peter Jackson first noticed this error while recording the Extended DVD Director commentary.
This was changed on the DVD, but on the original version of the movie, during the battle of Helms Deep the orcs launched ropes with hooks on them at the top of the wall. They started to hoist the big ladders with the ropes. Two scenes later they pushed the ladders the rest of the way to the wall but the ropes were not there.
When the Rohirrim are searching for the body of Théodred at the fords of Isen, Éomer rolls over the body of a Rohan soldier. Next to him you can clearly see a piece of yellow and black striped tape (in the bottom left corner), possibly a marker.
When Gimli kills the warg just after the battle on the mountainside, after Aragorn goes over the cliff, there are riders in the background acting out killing moves against the enemy. However there are no enemy present.
(flipped shot) When Aragorn is tracking Merry and Pippin from the orc pyre to Fangorn Forest, his ring (usually on his left hand) is on his right forefinger and his glove (usually on his right) is on his left hand.
When Gandalf is riding Shadowfax "bareback", there is clearly a saddle under his robes and his feet are obviously in stirrups. In some frames it appears to be a Western saddle, because as the robes flap around it, Gandalf and/or his stunt double appear to hold the horn.
When the Ents yank wood-and-iron buttresses from the base of a huge dam, water sprays out of the loosened stonework. But the sprays look and behave exactly like water squirting out of a tabletop-scale model, jarringly out of step with the high standard of modeling in the rest of the film.
When Theoden, Legolas, Aragorn and Gimli exit the front gates of Helms Deep before the battle, a SHOT looking out of the doorway appears and modern chalking on the gate is seen on the lower right of the SCREEN.
The goof items below may give away important plot points.
When Gamling and Hama ride ahead of the Rohan civilians to scout, and Hama's horse starts to get nervous and Gamling asks what's wrong, Hama is on the right and Gamling is on the left. Then in the next shot they switch places. And when the Warg jumps upon Hama they switch places again.
When Gimli enters Helm's Deep for the first time, he speaks to Eowyn about Aragorn's fate. Before she speaks, Gimli's helmet is on and his axe is covered in blood. After she speaks, his helmet is off and his axe is clean.
Near the end of the film, when Frodo and Sam are in Osgiliath, the chain around Frodo's neck with the ring on repeatedly switches between being caught around one of his buttons and hanging freely between shots.
At the very end of the movie, when Gandalf, Theoden, and rest of the main survivors of Helm's Deep ride over the hill together, and Gandalf says "The battle for Helm's Deep is over. The battle for Middle-Earth is about to begin.", the actor portraying Eomer is clearly not Karl Urban. This shot was done during pickups when Urban was not available, but WETA was supposed to cover up the actor's face with Urban's.
As Théoden, Aragorn and the others ride out of Helm's Deep at the end of the battle, when they ride down the "bridge", one of the computer generated Orcs, on the side of the bridge that is closest to the camera, goes straight through one of the horses before he is thrown from the bridge. Also (and conversely), horsemen in the back of the column slash with their swords at invisible targets.