Other mistake: Near the beginning there is a scene where they are launching a submersible with Lindsey and the seal team in it. Lindsey waits until the sub is dangling over the water then pulls a lever and the sub drops about 10 feet into the water with a big splash. Several problems: 1) Those subs are hugely expensive. They put them in the water very gently. 2) Those subs are so expensive that they don't risk having a release mechanism as depicted. They use a standard screw shackle to ring and would have to have a swimmer let them go. 3) Due to the buoyancy of the sub, falling that far to the water would give all passengers back injuries due to the sudden deceleration when the sub hits the water.
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: 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)
Suggested correction: They're on an emergency rescue mission and don't have time to be delicate with the equipment. Also, everyone in the sub is shown being thrown around when the sub hits the water. Hence the angry looks toward Lindsey.
They would still put the sub safely in the water. The first thing in priority in a rescue situation is scene and crew safety. If you damage the rescue sub or hurt the rescue team what's the point of the rescue. They would take the extra few minutes necessary to put the submersible safely in the water.