Continuity mistake: In "The Mummy Returns", we were told that the Scorpion King reigned before the Pyramids of Egypt were built. Yet in this film, where the Scorpion King is not yet a king, Layla talks about going to Egypt to see the Pyramids.
Other mistake: When Noah gets hit in the back with the arrow and falls to the ground, Mathias holds him up as he dies. When he dies, he's lying on his back, even when there is an arrow sticking a good six inches out of his back.
Continuity mistake: In the first movie, Mathayus has an older brother named Jesup who is killed by the villain. However, in this prequel, Mathayus has a younger brother named Noah who is killed by the villain, and there is no mention of Jesup whatsoever. Given that Mathayus and Jesup were supposed to both be warriors with the same tribe, it makes absolutely no sense that he isn't at least mentioned in the film, and the movie seems to pretend he never even existed.
Continuity mistake: In the scene when buying tickets to Egypt, a Celtic cross tattoo is visible on his left arm under his robe that does not appear in any other part of the movie.