Continuity mistake: When Sacagawea wakes up from her shipping container, the styrofoam popcorn comes out everywhere as she gets up. But moments before when it shows her being put into the box, there is no styrofoam, rather she's packed in with hay.
Visible crew/equipment: In the scene with Darth Vader and Oscar the Grouch, watch Darth Vader's eyes. You can see the light screens and crew reflected in his eyes in every shot.
Revealing mistake: When Amelia and Larry are flying, his hair doesn't move a single inch.
Continuity mistake: When Kahmunrah first appears on Archie Bunker's chair, the propeller beanie cap hanging on the side of the chair disappears in the close-up.
Factual error: When Larry and Amelia's plane takes off, the cables it is held onto easily rip off from the canvas. For security measures, a real cable would be made of steel, therefore ripping the structure instead of just snapping like a string.
Continuity mistake: When Larry's chauffeur takes him to the museum, the car passes way after a blue lamppost, but in the close-up it parks right next to it.
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.
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!" presumably referring to Robin Williams who plays Teddy. (00:51:40)
Continuity mistake: While Custer is guessing the Indian woman's name the monkey behind her appears and disappears.
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?
Suggested correction: While this could be a mistake, it could be an automatic scanner.
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: During the glowing torch commercial, the actor opens a drawer with metal stuff in, but in the wide angle a wooden stick appears.
Continuity mistake: When the cowboy and the Roman are standing on the crate, from behind you can see that the Roman's cape is long and covers part of the edge of the crate, but from the front is shorter and doesn't even touch the wood.
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: Amelia Earhart's lipstick goes from on, to worn off, to on again throughout the movie.
Continuity mistake: When Larry makes the batteries fall out of Brundon's flashlight, they fall all over the floor. During the rest of the scene, as Larry is walking away, there are no batteries on the floor.
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.
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: When Octavius and Jedediah escape through the hole in the metal container in the close-up, the shape of the hole changes in following shots.
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.
Suggested correction: The gate start to open right after pressing the buttons on the tablet, no magic words were needed. Kahmunrah was talking something with his eyes closed, but it had nothing to do with the gate opening.
Suggested correction: This mistake is not wrong however wouldn't you think they would have night guards in each of the museums, but no guard is ever seen anywhere.
Creating a silly, Deus Ex Machina solutions for obvious plotholes never resolves them. There is absolutely no way that these things would remain unnoticed by anyone. This entry is correct. This is indeed a plothole because it's much too confusing to be explained.