Visible crew/equipment: During the chariot race, just as Judah (stunt double) flips over in his chariot in the wide shot, a low angle camera is visible on the track under a canopy, at the right side of the screen.
Revealing mistake: In the shooting scene in the Mount Rushmore cafe, a boy in the background puts his fingers in his ears, because he knows the gun is about to be shot.
Visible crew/equipment: When the pilots are driving the plane and a spaceship pass them you can see a shadow of a microphone. (00:04:40)
Revealing mistake: A giant lizard is stepped on by Boone. The lizard's skin turns red after being stepped on. It becomes so red that a nearby rock begins reflecting the red light. (01:55:40)
Visible crew/equipment: When the severed head in Nora's suitcase has vanished, she shouts for everyone to get out and leave her alone. In the hallway when they disperse, as Loren and then Trent walk past Lance, something that shouldn't be there (it looks like fingers perhaps) pops up into view at the bottom, left corner of the screen. This is clearer in the colorized version of the film. (00:49:00)
Factual error: Captain Scott is sometimes seen with a Mk VI Webley, a historical anachronism as these date from 1915 onwards, whilst the film is set in 1905. This is also a continuity error as sometimes (particularly later in the film when he is fighting van Layden on the train roof) he now carries a much more period-correct Webley (MK V or earlier).
Continuity mistake: When Merryweather makes the dress blue a second time, it starts off on a ribbon that wraps itself around the dress waistline. The ribbon doesn't make it onto the completed dress.
Suggested correction: Hardly a mistake, since they're using magic and the dress changes multiple times.