When Nefetiri is watching Moses re-enter the city, she's holding a branch with yellow flowers which are unmistakably wattle flowers. This flower is native to Australia and won't be widely known about for another 3000 years.
When Ramses is threatening Dathan to tell him the identity of the "Deliverer," there is clearly a fuller (sometimes but erroneously called a blood groove) in Ramses' short sword. Egyptian swords did not have fullers. In fact, fullers would not be invented for hundreds of years.
During the end scene, Sephora says to Moses "You are God's torch that lights the way to freedom", but a different voice says "that lights the way to freedom." Yvonne De Carlo turned just as she said that part of the line, so it may have been dubbed.
Jethro tells Moses his people, the Midianites, were descendants of Abraham through Ishmael, "his first born." According to Genesis, the Midianites were descended from Midian, one of six sons of Abraham's second wife, Keturah.
When Nefretiri has Moses brought from the brick works to her barge, he is filthy, and he holds himself back from embracing her. At one point in the conversation, he grabs her shoulders, but leaves no marks on her or on her dress. Later in the conversation, he refrains from holding her again for fear of soiling her dress.
When the Pharaoh's chariots leave the city gates to go after the slaves, some shots of the chariots have long shadows, as if shot in late afternoon. But in other shots of the chariots, their shadows are short, as if shot in mid-day.
When Moses and Aaron appear before Rameses and Nefretiri in the throne room, and Moses says "let my people go" for the first time, Moses is standing in front of and between the ruling couple, with Nefretiri at stage left. As Nefretiri realizes it is indeed Moses, she looks up and to her left at him. The longer shot shows her correctly looking up and to her right at him, as he is between her and Rameses.
The Red Sea changes color many times while it's being parted. At times it appears blue, green, and even gray. In later TV and DVD releases, the Red Sea becomes deep blue in color without a hint of green.
As the sheep shearing festival, the wool is sold to Lugar, then Jethro's six daughters dance for Moses and the sheikhs. Moses leaves them to seek out Sephora. While they talk, many unshorn sheep are visible in the background.
After Rameses tells Moses that the slaves are free to go, the Hebrews line up along a road lined with many identical sphinxes, which the narrator identifies as the "Avenue of the Sphinxes." That road still exists, in the ancient Egyptian capital of Thebes, now known as Luxor. Yet pyramids are visible in the background. Those pyramids are in Giza, which is near Cairo, about 315 miles (500 km) north of Luxor.
On the night of the 10th plague, the shadow of The Destoyer appears over a 3/4-moon. It should be a Full Moon. Passover (as this night is now celebrated) starts on the first Full Moon after the Vernal Equinox.
In their last scene together, it is uncertain whether Ramses II will kill Queen Nefertari. In historical fact, Ramses built an elaborate temple to her - the favorite among his many wives - at Abu Simbel.
When the obelisk is about to be raised, a worker waves a blue banner against the blue sky. Bits of it vanish as it moves. This would have been because the invisible parts were catching enough light that they would match the background. When the special effects team was painting out the background to insert the sky as an underlay they were not able to determine what was sky and what was banner so they accidentally painted out the lighter elements of the banner.
When Pharaoh decrees the slaughter of the Hebrew sons, he adds "So says Ramses the First." Ramses would just have been called Ramses at that time as Ramses the second would not be around for another forty years.
Miriam tells the women at the well to fill their jars, because there will be 7 days without water. Pharaoh's jar of water turns red. The Hebrew women's water did not turn to blood was because God exempted the Hebrews from the plagues.
Differences from the source material, and most other historical inaccuracies, are exempt from being listed as goofs, especially when they're caused by dramatic decisions, reliance on ceremonial traditions, or Renaissance-Baroque artistic depictions.
The Red Sea just parted, the sea floor should be mud or wet sand, yet it is completely dry. This is not a goof; it is a miracle. The book of Exodus, on which the movie is based, says multiple times that the land was dry.
When the Hebrews are leaving Egypt, a man throws a golden calf statue to a small boy, who catches it with no problem. If this were made of solid gold, this could be a mistake, but if it were made of wood covered in gold leaf (which was a common method) it would not have been very heavy.
As Moses was completing the building of an Egyptian city, and called for a blue pennant, the guard waves a blue flag in front of the backdrop, and the flag is filtered out and becomes transparent, alluding to the fact that there is in fact a blue-screened backdrop and not an actual city behind them.
During the chase in the Red Sea, the lead chariots ride on ground neatly grooved with wheel tracks, with no evidence of the footsteps made by thousands of slaves and animals. A shot of the slaves exiting the Red Sea reveals how trampled the ground should have looked.
As Moses leads the Israelites through the parted Red Sea, he stands on a tall outcropping of rock on the far end, to encourage his followers who are still making the journey through. As his people reach the other side, Pharaoh's forces approach quickly. Moses gives the signal, and the parted Red Sea collapses onto the Egyptian troops, while Pharaoh stands on a nearby rock. The remains of the gigantic wall of water sweep onto the ground, surrounding his position. Two large, obviously fake boulders float on top of the water, landing on the beach on the left of the screen. It could be argued that the force of the onrushing wave merely swept the rocks along. While a large amount of swiftly moving water can change entire landscapes, solid objects such as stone would move along the floor, not on the surface.