Continuity mistake: In the opening sequence Sacajawea is placed in a crate of tan, straw-like packing material. When Larry visits the museum a few hours later, Sacajawea emerges from a crate full of white packing "peanuts" (styrofoam pellets).
Continuity mistake: In the scene where Larry and Amelia escape into the VJ Day photograph, Larry is seen speaking to a sailor in dress blues. Throughout the exchange the rating badge on the sailor's arm changes from crossed keys, the insignia for storekeeper to lightning bolts, the insignia for radioman several times.
Other mistake: When Larry first enters the main storage room, he has to go by the guard Booth. A voice says "ID" then acknowledges that it's "Brundon, later dude". When it shows Larry from behind it shows a clear shot of the inside of the entire security room. It is completely empty. Did a ghost ask for the ID?
Other mistake: In the fight scene between Larry and Kahmunrah, Larry throws the tablet to Amelia Earhart and she opens the gate, but she didn't say the magic words to open it or even worse she doesn't know those words as Kahmunrah.
Factual error: Larry and Amelia Earhart both fly the Wright Flyer using a stick control. It was actually controlled using a mechanism attached to the pilot's hips whereby he could turn the aircraft by shifting his body from side to side.
Factual error: On the shoulder of the Tuskegee Airmen, their 'American Flag' patch is seen having 50 stars. At the time of WWII, the US flag only had 48, and 48 would have been the number they'd wear.
Audio problem: When Larry sees the bust of Theodore Roosevelt in the Smithsonian, he calls out "Teddy!" But if you listen carefully after that he says "Robin!" probably referring to Robin Williams who plays Teddy.
Continuity mistake: The way crates are placed differs enormously between the moment before and after the dinosaur throws Ben Stiller flying. Watch the crates on the back: First they are spread apart, perpendicular to the animal, but when Stiller lands they're parallel and close together to hide the safety crash mat in between.