(at around 1h 2 mins) The amount of fire extinguisher foam on Larry's face changes frequently.
(at around 35 mins) In the miniature people scene, after Larry breaks free from his upper body restraints, the roping around his ankles is still in place. In the shot just before the Romans attack him with fire balls, the ropes are shown around his ankles, still in place. However, after the Romans begin to attack him, Larry is able to get up and run away with ease - there is no shown attempt to break the restraints around his ankles.
(at around 32 mins) When the Mayans attack Larry by shooting poison darts at him, the darts leave two very large welts on his face that also appears to have caused him to lose feeling there as well. But as the camera scene cuts to him trying to defend himself from a second, larger attack the welts are gone from his face and he takes about a dozen darts in his hand, this time with no apparent effect.
(at around 8 mins) When Larry and Nick are in Central Park at the beginning of the movie, the building with two towers is visible behind Larry. When they turn to leave the park, the building is still behind Larry. However, in the immediate scene following, the same building is now in front of Nick and Larry.
(at around 23 mins) The T-rex picks the desk, and drops it. It falls vertically. But when we see the hall in full, the desk is lying near the wall, on its side.
The plot depends on sunset occurring late in the evening (well after the museum closes) and sunrise occurring early in the morning (long before most of the city awakes for the day). But it's winter in New York, so sunset and sunrise would be during morning and afternoon rush hour.
(at around 25 mins) When Attila the Hun sticks his head between the elevator doors, the mechanism of the elevator would force the doors to open, rather than continue to close.
(at around 1h 30 mins) The stagecoach wheels are shown skidding in the snow, although the horses were stopped by command and the brakes would not have been applied.
Theodore Roosevelt was known to have a high-pitched, squeaky voice due to being a severe asthmatic. However, Teddy explains that he is a wax figure of Roosevelt designed to appear very heroic, so it makes sense that he'd have a deeper, more resonant voice, not unlike Robin Williams.
The correcting spelling and pronunciation of the name Sakagawea/Sacagawea/Sacajawea are unknown, hence the wide variety used in this movie.
Anything relating to what the magically-enlivened museum pieces can or cannot do. Since they are fantasy beings, they can do whatever the writers say they can do, even when the logic appears contradictory (e.g. Teddy knows he is a mannequin, while Sacagawea does not).
The tablet was supposed to be made out of 24k gold (100%). But the weight of pure gold is 19.3 kg/liter, and Larry's son wouldn't be able to carry the tablet as easy as he does.
(at around 35 mins) The Roman troops shoot flaming arrows at Larry, but his clothes show no burn marks.
(at around 30 mins) When Dexter bites Larry on the nose there aren't any bite marks and no blood either.
(at around 50 mins) When Reg is in the security office copying Larry's house keys, the pad he uses has the imprint of a key on it before he uses it.
(at around 17 mins) When Cecil hands Larry his "torch" on his first night, he hands it to him lens side down, when Larry takes it it is lens side up (flipped).
When Larry is trying to convince Rebecca that the museum comes to life at night, a crew member is visible behind her.
When Larry and Rebecca were talking outside, you can clearly see a mike drop down in the shot, bob up and down and then taken out of the shot. At the end with career day at school the mike appears again.
Dexter the Capuchin monkey "speaks" like a chimpanzee.
(at around 46 mins) Sacagawea wasn't a tracker, she was only a guide and translator. Her husband, Charbonneau, was the tracker on the Lewis and Clark expedition.
(at around 46 mins) The Hall of African Mammals includes both Dexter the Capuchin monkey (from South America) which is a mammal but not African, a snake which is a reptile, and an ostrich (bird) which is African but not a mammal.
(at around 51 mins) Larry refers to the Neanderthals as the first people to build fires. In fact, Homo erectus achieved this before the Neanderthals.
The "Museum of Natural History" has exhibits of modern historical figures and events.