Factual error: The giant squid's tentacles aren't shaped like ones in the real world are.
Factual error: During the undersea trek, a nurse shark chases Ned and Conseil. Nurse sharks are actually pretty harmless and shy of divers.
Factual error: When they first arrive on the Nautilus, they look out the large porthole and see the crew on the bottom of the ocean burying one of the crew, but the ocean would be much deeper than that, since the Nautilus is at the surface.