Factual error: Dexter the capuchin is in the African mammal display. Capuchins come from South America.
Plot hole: Christopher Columbus speaks Italian while the Huns supposedly speak their native language. Shouldn't Octavius and his Romans speak Latin? (00:34:50)
Plot hole: Why does Larry wait until the Mayans come alive to lock them up? I know he's allowed to be stupid but he had a lot of time to sit and do nothing and I can see no reason to wait.
Continuity mistake: When the T-Rex is going after Larry, Larry is behind a desk. The T-Rex bangs his head on the desk and then lifts the desk and throws the desk. A few scenes later the desk is back in place and there is no mess from the papers that were there before. (00:22:50 - 00:23:40)
Suggested correction: The desk is at the opposite end of the hall, the desks in shot were never touched by T-Rex.
But roughly at 40m the desk stands well again. Maybe end of the night magic - but the desk is in place without being touched by anyone.
Continuity mistake: When Larry does the magic trick with the disappearing handkerchief, the amount of coloured handkerchief visible out of his thumb changes massively between shots. (00:59:00)
Continuity mistake: When the Neanderthals throw the foam on him, it noticeably changes shape and size throughout the next few shots. (01:02:05)
Revealing mistake: In the park after the bad guys have been defeated and everyone starts returning to the museum, watch the T-Rex closely. In the overhead shot, he seemingly "floats" right through the branches of the trees which he normally would be moving. (01:34:50)
Continuity mistake: When Larry first meets the Easter Island head, he is talking to him from about 5 feet (or more) away. When it cuts back to him after the shot of the people chasing him, he is just inches away from it. (00:24:50)
Factual error: Sacajawea was not a "tracker." Lewis and Clark hired her husband, Toussaint Charbonneau, and her as interpreters, because she spoke the Shoshone language. (She was 16 and pregnant at the time).
Revealing mistake: When the T-rex launches the table away, a couple of papers on it don't move a single inch, revealing they're glued to the table.
Continuity mistake: Sacajawea is pushed down by Teddy and falls face-up, but lands face-down a shot later. Though she could've turned around while falling, she only has half a second while freefalling in panic, so it's quite impossible for her to turn around.
Suggested correction: It's impossible to say how exactly she falls in that moment, she could turn pretty much everywhere when she was out of frame.
Continuity mistake: When Larry notices the caveman's footprints leading to the open window and goes to investigate, the footprints are gone in the next shot. (01:05:25)
Visible crew/equipment: When Larry and Rebecca (in her red coat) are outside the museum and she is giving him information about the exhibits, there is a boom mike visible in the top part of the screen for a brief moment after they cross the street. (00:47:30)
Continuity mistake: When Larry is explaining to Rebecca how the museum comes alive at night, her purse straps are alternately crossed and uncrossed on her shoulder. (01:11:25)
Continuity mistake: When Larry lifts up the cowboy and the roman emperor and places them on the bench, they move closer together between shots. (00:53:20)
Factual error: During one of the first scenes with Teddy Roosevelt he has a small "2" on his collar above his Cavalry crossed sabers. However, his "Rough Riders" were in the 1st Cavalry Regiment. Later in the movie he's wearing the correct "1" there. (00:36:20)
Revealing mistake: Towards the beginning of the film when Ben Stiller looks at the photo at him and his son, you can see that the photo is a fake. Ben and his son cast a shadow on the shadow behind them.
Continuity mistake: The epaulets on Larry's normal jacket disappear and reappear between shots.
Continuity mistake: When Larry tells Rebecca that the museum comes to life, they are in front of the Neanderthal display. But when Rebecca leaves, they are in front of Teddy Roosevelt.
Continuity mistake: In the end, when Larry meets up with Teddy Roosevelt, during that whole scene, the people in the background change positions, especially the guards in the blue cape.
