The sprinklers in the museum are soaking everyone and the mayor's wife's hair is wet and hanging limp down on her head. When the group starts down the stairs she is briefly shown with her hair now styled and only her face is wet.
During the autopsy scene, the ties on the medical examiner's mask change between going over the microphone headset and going underneath.
The night of the Gala, after the search light is turned on; the scene shows the Partygoers walking the red carpet & ascending the stairs of the Museum.
But when the camera then pulls back, there is no line of People entering the Museum. And in later scenes, the Red Carpet is gone all together .
In the book by Douglas Preston and Lincoln Child, the monster has been in the museum's subbasement for around seven years, making the lair filled with either partially or fully decomposed skeletons completely plausible. However, in the movie they change the duration to only six weeks. The lair they find in the movie with tons of skeletons doesn't connect with the time it took for them to become that decomposed.
On board the Santos Morales, the detectives find big blood stains on the walls and floor. The blood is clearly dry, but is is still bright red, and is evidently paint. Dry blood is that old should be brown.
There is no such species as Rhinocerus Megarhinos.
The tank into which Margo falls only contains hot water, used to loosen skin from a carcass. At the time she enters this tank, it is switched off and the water is cold.
The movie places the first murder and the break-in for the crates on the same night. If the Kothoga had gotten to the crates, why did it need to kill. The fungus on the leaves were believed to be parasitic so they were destroyed along with the crates they came in during the day. Since the crates were destroyed, the Kothoga killed the guard at night.
When the dead body of a cop falls from the ceiling during the gala night, the wire from which it is suspended can be seen briefly.
On the Silicon Graphics computers, one of the sound effects heard is a floppy disk drive access sound from an Apple Macintosh computer.
Dr. Whitney's crates containing the rare leaves are being shipped from Brazil, and the ship on which the kothoga journeys is "registered out of Brazil." Yet in the scene where Dr. Whitney races to try to keep the crates from shipping out, the captain and the dockworkers and crew are speaking Spanish rather than Portuguese.
The trip of the Santos Morales from Brazil to Chicago is not possible, let alone in six weeks. Although Lake Michigan is technically connected to the Atlantic Ocean, the ship would have to fly through Niagara Falls in order to get to Chicago. This is possible in the book, as it takes place in New York.
The ship's captain at the beginning is supposed to be speaking Brazilian Portuguese. In reality, he is speaking gibberish, mixing Spanish and Portuguese with a very basic grammatical structure.