Dr. Quest and Race exit their plane wearing holstered guns. These guns and their holsters disappear and reappear over the rest of the show. (Specifically, at dinner, Race's holster seems to have disappeared; Dr. Quest still has his up until he throws a lantern at a porthole. When Race opens the door to look outside, his holster is back, but back in the galley, both his and Dr. Quest's holsters are gone. When Race is later searching through the ship's hold, the holster is back at his hip. Back on deck, Benton's holster returns as well, up until he puts his hand on Jonny's shoulder, but when he stands with Race, they're both wearing holsters.)
When Hadji takes the picture, he is using a camera similar to the Polaroid 300 series, which were only able to take pictures with the bellows extended. With the camera still folded into its storage configuration, he would have been unable to operate the shutter; with the bellows extended, he would not have been able to obscure the lens with his finger.
The flares fired by Bannon and Quest are depicted as exploding. Maritime distress flares do not explode; they burn for anywhere from two to six minutes.
Speculation arises that the creature was disturbed from the deepest depths of the sea floor by recent heavy storms. No storm is so great that it can affect sea or ocean floors at profound depths. This explanation doesn't hold water.
Jonny and Hadji search for Bandit in the hold and find him hiding inside one of the "coffins." It is not explained how this dog was able to get inside one and pull the lid over on itself.
When Jonny looks at the picture Hadji took, he says, "It's a great picture - of your thumb." However, the closeup of Hadji snapping the picture clearly shows that it is the middle finger of his right hand in front of the lens.
On fire, Charlie jumps into the sea but quickly winds up surrounded by sharks. Race tells him to keep splashing while he shoots the sharks with his gun. That's two things he shouldn't do. Splashing tells sharks an injured fish is nearby - easy prey. Bullets, if piercing any of the sharks, will put blood in the water, causing sharks to enter into a feeding frenzy, attacking everything around them. Instead of helping Charlie, Race's advice and actions would surely get Charlie attacked by the sharks.