Continuity mistake: In the scene where Jonathan picks up the scarab, it breaks open and the beetle inside starts to crawl under his skin. We see Brendan Fraser tear Jonathan's shirt and cut the beetle out of him. However, in the very next scene, we see Jonathan walking into the temple, his shirt is intact and there is no blood to be seen.
Continuity mistake: In the scene in the library, when Evie is putting back the books. She leans over to put the book back, but it falls to the ground and she is balancing on the ladder. When the camera cuts back to show the whole ladder, the book is nowhere to be found on the floor.
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: On the DVD version of the movie there are some deleted scenes - one would have explained two mistakes that occurred towards the end of the movie. Mistake one was that there was a hole in the ground when Jonathan and Rick are at the base of the statue of Horus. You can see the hole clearly when Rick lights the TNT - but without the missing scene there is absolutely no reason for that hole to be there and it just sort of appears.
Factual error: The city at the beginning of the film where the Pharaoh lives is named as Thebes, and you can see the Sphinx and the pyramids in the background, but these are in Giza, not Luxor, as Thebes is now called.
Factual error: I counted five canopic jars, one of which has the head of a lion. In ancient Egypt there were only four canopic jars - Hapi, the baboon-headed god representing north, Imseti, the human-headed god representing south, Duamutef, the jackal-headed god representing east and Qebehsenuef, the falcon-headed god representing west. None have lion heads.
Factual error: Due to the Earth's rotation, the mirror system used to light the tombs would only provide light for about 4 minutes before needing readjustment (tested by the Mythbusters). This would be fine when there were plenty of priests around to adjust them constantly but the light level never changes even though we see Rick and Evie for several minutes at a time.
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.
Continuity mistake: When O'Connell and the others are escaping Imhotep's crazed followers they crash the yellow car and abandon it. The next morning they are seen arriving at the old RAF pilot's camp in the same car which shows no sign of damage. Were all of the cars in Egypt yellow and the same model or did they sneak back to retrieve that one taking it to an all night Egyptian body and fender shop before setting off to rescue Evie?
Continuity mistake: Ardeth Bay removes the Lewis gun from Winston's plane after it crashes in the desert. If you look at the gun, it has the correct 97 round drum (it's really noticeably thick) with a leather carrying handle on top and no paint marks on it - this is correct for aircraft use. Aside from the fact we never see Ardeth Bay remove any spare magazines for it (which would also have been of the 97 round variety), which would have left the gun with little if any ammunition after shooting at the wall of sand, by the time they all arrive in the treasure room, the magazine suddenly changes to the 47 round variety (thinner than the 97 round magazine), which does not have the leather carrying handle, and has the painted marking on the top of it to enable the magazine to be more easily changed at night.