Other mistake: During the submarine interior scene, there are several dead seamen shown floating about. One of them is pretty close to the camera and floating with his eyes open. He blinks before the shot ends.
Other mistake: When the water tentacle enters the rig, in one shot in the 4:3 version of the film on video you can see that the tentacle is a superimposed special effect because of the dead straight line where it is supposed to have come out of the water.
Other mistake: At the end of the film the NTI's entire ship ascends from the abyss to the surface. What happened to the rest of the sea floor that Bud, Lindsay, and Coffey had to race over during their battle? All of that seems to disappear when the mothership comes up.
Suggested correction: Maybe I didn't understand what you are describing as an error. Only the ship ascends, the sea floor stays, well, on the sea floor. Since the ship is huge and has been there for a while, it is likely that a large part of the ship was covered by silt, making it appear to be sea floor.
Other mistake: When Ed Harris is dropping down the Abyss there are a couple of time that bubbles come out of his mouth or can be seen in his nostrils, even though he is supposed to have been breathing liquid for quite some time. (02:13:28)