When Moses is dragged by the camel, his arm is looped through a brown bag filled with water. Just before his head hits the well, his arm is looped through a red strap.
During Moses's nightmare, Miriam is wearing pink (like she does throughout the rest of the film). When they arrive at the water's edge and the adult Moses sees his mother put his baby counterpart in the basket, Miriam is wearing orange.
When the plagues destroy Egypt, not a lot of monuments are shown being toppled. However, in the song "When You Believe", when the Hebrews are walking through the ruins of Egypt, there is far more damage and destruction of Egypt that what was seen in the Plagues. However, the entire breadth of the plagues could not be shown since, in the record of them, the plagues last a lot longer than a few minutes, leaving the possibility that we didn't get to see all of the destruction.
After Moses and Tzipporah are wed, they go off to dance. As the camera starts to zoom between them towards Jethro, the animation of Tzipporah freezes.
When Moses' mother, brother and sister are hiding from the Egyptians, they see a group of soldiers running past. However, the only things that pass are the soldiers' shadows - the soldiers have been left out.
At the end of Moses' dream sequence, as he falls into the Nile River, he passes a sun-disk with rays that end in the appearance of human hands. This method of depicting the sun is more typical of the reign of Akhenaten (1351-1334 BCE) in the 18th Dynasty and the Amarna period. This is so because of the quasi-monotheistic "heresy" of Akhenaten in which worship of the sun god became prominent. This scene, however takes place during the 19th Dynasty reign of Seti I (1294/1290-1279 BCE).
While Rameses and Moses are fleeing from the temple on their chariots their horses neck bands are missing.
Some of the Hebrews can be seen seemingly drinking water from the Red Sea near the end of the movie.