Plot hole: Property is destroyed, museum windows are crashed through, a giant octopus splashes about in the National Mall's reflecting pool, and even the statue of Honest Abe at the Lincoln Memorial comes alive. With all this occurring, not a single D.C. resident seems to notice and nary a single police officer turns up to investigate the goings-on.
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?
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.
Continuity mistake: When Ben Stiller is dropped off from the red plane in the middle of the street, the streetlights in the background are yellow for a moment, then switch to another angle and they are green (without adequate time to switch back), then they constantly switch between green and red depending on the camera angle.
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.
Continuity mistake: When Jedediah is in the hour glass, he is in the lower chamber, and the area between is too small for him to go through. When the minions are returning to the portal, in a close up he is obviously in the top chamber, only to return to the bottom when Octavius breaks him free.
Plot hole: Before Amelia Earhart flies herself and Larry back to NYC from Washington D.C. Larry says that there is an hour of darkness left. The time needed to fly from Washington D.C. To NYC and back is well over an hour, so it's not possible to make it in the time given and Amelia would have turned to dust.
Add timeA Demon
Continuity mistake: When Custer is explaining how they will yell "Attack!" before attacking and Sacajawea questions the veracity of this plan, she is first in front of the caveman, etc. (with her back to the door of the box-crate) and then with no one behind her (with her back to the side of the box-crate).
Continuity mistake: In the conclusion of the Brandon scene, as Larry is leaving, Brandon is shown in the background trying out the flashlight moves Larry had just done. As he does this, Brandon is walking toward the left in this shot, just beyond the Kahmunrah gate exhibit sign. The next shot is of Larry and the stolen guard pass. When they flash back to Brandon, he is walking in the same direction, but has not yet passed the sign. The order of the shots was simply mixed up.