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.
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.