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: 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.
Other mistake: When Larry takes Jed back to his miniature city, in the shot where the T-Rex almost hits Larry, watch Teddy's' horse. His head moves, following Larry and the cameraman. This cannot happen as the horse and Teddy had been already transformed into statues. (00:42:00 - 00:43:00)
Suggested correction: The horse's head moves way before the point where Teddy turns back into a statue in a very close view.
Continuity mistake: When Rebecca leaves the Museum after sitting in front of the Sacajawea display after Larry asks her to leave as he's closing up, from the internal shot of when she's leaving the Museum she exits through the middle rotating door but on the outside shot she is seen leaving from the door on the right hand side of the Museum.
Suggested correction: She is coming out from the same door in both points of view.
Suggested correction: She doesn't exit the middle door. She exits the door on the far left (you can see the 3 red carpets laid out in front of the doors and she's on the 1st/3rd one). The area to her left isn't an exit door.