There is a Garfield plush toy stuck to the window of the SEALs' quarters, which is present in every single scene except while Hippy is spying on them through the window with Big Geek.
The cuts that Coffey gives himself, disappear, reappear and change in number and position many times.
Beanie the rat does not produce visible air bubbles while breathing the oxygenated fluid, yet later, after Bud starts his fluid-breathing dive to the bottom of the trench, he is seen emitting lots of bubbles as he breathes.
The alien vehicle approaches the Montana on a course that nearly leads to a head-on collision. It is moving at 130 knots and the sub is moving toward it, yet it takes about 13 seconds for the range to close from 200 to 100 yards and another 3-4 seconds to come down to 60 yards, corresponding to a combined speed in the range of 13 to 20 knots. An object moving at 130 knots will go about 950 yards in 13 seconds, nearly half a mile (2025.37 yards in 1 nautical mile - 1 nautical mile = 1.15 statute miles or 1.852 kilometers)
During the submarine chase sequences, Coffey smashes a tape player with his elbow. A few shots later, it is back in one piece.
At the depth the crew is diving, they would be breathing a mixture of gases to include helium. Regular conversations while breathing this mix of gases results in the typical "helium speech," like if you breathed in a helium balloon. Normal conversations during the entire film at depth would have been with helium speech, and not regular voices.
For operational security reasons, Navy SEALS never acknowledge each other by rank, nor do they use their surnames. Everyone on a SEAL team, even the officers, only address each other by first name.
When the divers are swimming, you can see bubbles with every breath, meaning that they are on an open-system (i.e. scuba). However at that depth (2000ft), a standard scuba tank would be exhausted in under two minutes, or much less with any kind of exertion.
Coffey (Michael Biehn) wears a ball cap with the word SEAL on the back. SEALs are a clandestine unit and would never identify themselves in such a manner.
No military service would ever describe a course as oh-six-five. "O" is an alphabet letter. All courses with a "0" digit are called out "zero".
While treating Jammer, Ensign Monk says that he is "just a medic, which is mainly about patching holes." SEAL medics have previous medical training before being trained as combat medics, and since they work with a scuba diving unit, he would also be well trained in any facet of diving related injuries and or maladies. However, Jammer is in a coma, and unless it is a medically-induced one (which it is not), he will have to wake up on his own. No medic can treat a natural coma, no matter how well trained.
While a defibrillator is of no use if a patient is truly asystolic, a patient in a "fine v-fib" rhythm can appear to have flatlined but still be revived with the paddles. Therefore, when in doubt, Advanced Cardiac Life Support guidelines call for administering the shock, though it's not the treatment of choice.
As Virgil descends into the abyss near the end of the movie, he is told he has broken the world record for depth. When he types his reply 'call Guiness'. Although Guinness requires two Ns, Virgil admitted earlier he was a bad typist. He also makes numerous other spelling errors during his descent.
While Lindsay's drowning scene in the submersible was obviously played for dramatic effect, if they were really concerned about reviving her it would have made much more sense for her to take a deep breath and for Bud to then immediately began towing her back to the rig. She would have then drowned on the way there and there would have been less time between her drowning and the start of the resuscitation attempt, thus increasing the chance that she would be successfully revived.
Soon after Virgil begins his descent into the abyss, Linz informs him that he's broken the world record for the deepest sea dive. He smiles, which causes air bubbles to come out of his nose, even though he's supposed to be breathing liquid oxygen.
When they are reviving Lindsey, there is one point where Bud
slaps her and tells her to "fight". The moment before he slaps her you can see her blink in anticipation of the slap.
When Bud and Jammer first enter the Montana, a corpse floating in the foreground clearly blinks his eyes.
When Coffey's submersible bumps into Lindsay's, she, Virgil and the submersible are shaken violently, however, the yellow rope coiled in the background remains stationary indicating the effect was achieved by shaking and tilting the camera.
When speaking to his commander, Coffey announces "...could've been a Russian bogey." A "bogey" is a radar or visual contact whose identity is unknown. Thus, knowing that "a Tango and a Victor (Russian submarine)" were spotted within fifty miles, all Coffey had to say about the NTI incident was, "It could have been a Russian sub" or simply, "It could have been Russian."
At the end, when the alien ship has surfaced, and all human surface ships are sitting on top of the alien ship, during the wide angle shot, the submersible drilling platform, Deepcore, is missing from the scene.
When Bud and Coffey are fighting at the pool you can see a hand, on the right side, reach in and grab one of the dangling wires and pull it out of the way. This happens when Coffey, shown from behind, tries to stab Bud for the second time.
When Coffey is looking out of the window after the warhead is discovered, it is possible to see the hand of the camera operator press off the side of the window.[special edition only]
During the climax scene, when Bud tells Lindsey "Don't argue with me, just put it [the diving gear] on", there is a crew member wiping the camera lens twice. Apparently, during editing James Cameron liked this take so much that he just kept it in the final movie.
When Bud is staring at the warhead while using his liquid breathing device, you can see the air bubbles from the cameraman reflected in his visor.
Two white plastic buckets are visible on the ocean floor at the start of the submersible chase (screen left in the shot of Coffee's submersible turning while descending from the moon pool.)
The Statue of Liberty does not face the Verrazano Narrows Bridge.
The Benthic explorer and crew are drilling for oil off the coast of Florida, where Cat says there is a pit 2-1/2 miles down. There is not a ridge or a trough anywhere near that deep near Florida, with Cuba "only 70 miles away," as the TV reporter said. The only trough even close to that depth is some 700 miles to the south of Florida, the Cayman Trough, which is even further south of Cuba and is closer to Jamaica than anything, and another ridge near Great Abaco, some 350 due east of Florida, both of which were not consistent with the Benthic Explorer's given location and the rig below it.
The crew (except Bud) gives up on trying to revive Lindsey after only a couple minutes, when they should have known that cold water drowning victims can be revived even up to two hours after drowning.
The primary mission of a ballistic missile submarine is to hide and remain hidden. The aggressive chasing of an unknown target, which ultimately led to the crash, is completely out of character and most likely a direct violation of orders. They would be far more likely to have slowed down, so as to reduce their noise output and become more stealthy, then to try and sneak away.
While in the battle between the submersibles, Ed Harris' character keeps saying "Left" and "Right". As someone who's spent time at sea, he should be saying "Port" and "Starboard".
The DeepCore crew had no idea what kind of triggering devices that Coffey had rigged to the nuclear warhead, nor would they have known how "vulnerable" or "touchy" he had made the bomb, so they would not have just randomly sprayed dozens of bullets around the Moon Pool in hopes of disabling Flatbed, since they might also hit something on the warhead and blow everybody sky-high.