Other mistake: In the scene with the plane that is attacked by the mega shark and subsequently crashes, the camera focuses on one character in particular- a man who states he is "getting married in a few days". It is assumed when the plane crashes that everyone on board dies, yet in the very next scene this man walks behind Deborah Gibson's character as an extra.
Continuity mistake: The aircraft used to deliver the pheromone lure to the creatures starts out as a F-15, then after a few shots it becomes a F-18 then back to an F-15 for a few more shots, then back to a F-18 and is finally a F-22 when knocked out of the sky by the giant octopus. (00:44:00 - 00:45:30)
Revealing mistake: Just after the submarine crew see all the whales passing them by, the shot switches back to the helicopter and all the dials on the console. If you look closely, you can see that the image has been flipped as all the words and numbers are the wrong way around. (00:05:20)
Factual error: The "US Lead Destroyer" attacked by the megladon is the Iowa class battleship USS Missouri (BB63). (00:29:00 - 00:31:20)
Continuity mistake: During the opening scene, Deborah Gibson's fingernails keep changing from being painted to not painted.