Continuity mistake: In the scene where Imhotep's priests first pop up, Jonathan is on Rick's left, and the guy in black is on his right. But in that split-second shot that shows them starting to fire, they are on the opposite sides. [In the director's commentary he does mention this but says it's because they had to cut some scenes out due to time, still a mistake but has a reason.]
Continuity mistake: In the scene where Evie & her brother meet Brendan's character for the first time, the guards bring Brendan out with both arms shackled together in front. After he kisses Evie the guards pull him away and one of his hands is suddenly free - he quickly tucks it behind his back as he's dragged off.
Visible crew/equipment: In the scene where Brendan Fraser and the Americans are talking in the bar before the water turns to blood, there is a shot of two of the Americans and Fraser. Off to the left, you can see a hand dip in and out of frame. This is the First AD's hand. The director said he was checking his watch.
Continuity mistake: When Rick finds Beni in the office, after Beni says "I am immune", Rick slams him into a pile of boxes, sending stuff flying. Nothing is visible behind Beni's head, just a sheet of paper at neck level. Then after Rick says "immune from what?" we cut to a different angle - boxes are now piled much higher behind Beni, and there's a bit of paper resting on his hat.
Continuity mistake: In the scene when they are driving through town trying to escape the mob, the car crashes, and you can see that its lights are on. When Rick helps Evie out of the car, its lights are off. A few seconds later, you can see in the background that its lights are on again.
Revealing mistake: When Imhotep transports Evie, Beni and himself back to Hamunaptra, Evie hears the plane and looks up. Before she states "O'Connell," you can see the letters and numbers on the side of the plane are backwards, like a mirror image - it says "B5538" backwards, which resembles "BE228" (no mirror).
Continuity mistake: When they show Anck Su Namun committing suicide at the beginning, when the Pharaoh's guards show up she whips around to face them and all of her hair goes over her left shoulder. None is left on her right shoulder. However, in the shot from the front, she has half of her hair over each shoulder.
Continuity mistake: The pharaoh realises that his mistress Anck Su Namun was touched by another man because the body paint on her left shoulder is smudged. However, the way it is messed up differs drastically between when it was being smudged by Imhotep and when the pharaoh points to it.