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Continuity 

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)
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The Explorer has its name written on its side in some shots, but not in others.
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Lindsey's hair during the drowning revival scene.
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When the rig is pulled to the edge of the abyss by the crane the rig can be seen tilted, yet interior scenes and later exterior scenes remain level.
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The door that Bud, Catfish, and Sonny close after saving Bud from drowning appears to be hinged on one side of the hatchway then the other.
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During the submarine chase sequences, Coffey smashes a tape player with his elbow. A few shots later, it is back in one piece.
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The cuts that Coffey gives himself, disappear, reappear and change in number and position many times.
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When they find the Montana, it looks like it's tilted (banked) to one side by about 50 degrees or so. A few shots later, it looks more like 70 or 80 degrees, and in the interior shots it looks more like 20 or 30 degrees.
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When the crew have to cut some power to facilitate communications, a light is turned off behind Lindsay. In a subsequent shot, the light is on again, then off a few seconds later.
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Right before Coffey and Bud start their fight at the Pool, we see close-ups of each of them. In the first close up of Bud, he has a swollen eye, but in the next one it has disappeared.
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When Coffey closes the Moon Pool door on the entity, the tail end breaks and splashes to the floor. After the same happens in the room with Lindsay and Bud and we return to the Moon Pool, the back end half is intact and "stares" menacingly at Coffey before plunging into the water.
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Just before Bud touches down at the location of the warhead, his light flare is over 2 feet long, but when he touches down just a few seconds later the flare is burning out and is under 1 foot in length.
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Crew or equipment visible 

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]
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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.
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When Coffey is assembling a sub-machinegun there are only two people in a small room, but a third person can be seen on the right for a moment.
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After the submersibles battle with Coffey, Bud is swimming back to the rig with Linz and you can see air bubbles rise behind them, most likely from a hidden safety diver.
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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.
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When the water creature is exploring the war head you can see the square reflective mylar sheet with a stick to agitate it to give the rippling light effect.
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Errors in geography 

The Statue of Liberty does not face the Verrazano Narrows Bridge.
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Factual errors 

Even if the wind force on the Benthic Explorer is enough to drag the massive rig along the seabed, it could never be enough to accelerate it from rest to at least 1 mph in less than a second when transmitted over an umbilical cord at least 2,000 feet long. No matter how strong the cord is, over that length it would have to stretch to some extent and this would limit the acceleration.
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The drilling rig's submersibles are launched from a moon pool and the air inside them must therefore be at the same pressure as the water at that depth. Consequently, when Bud and Lindsey are endangered by a leak, the flooding should rise only as high as the leak, not right to the ceiling.
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Although, of course, all the equipment and terrain is fictional and only subject to fictional physics, it is intuitively extremely unlikely that something the size and weight of the fallen crane could pull something the size and weight of the rig along the sea bed, especially when the cable is draped over the edge of the cliff and the crane is presumably bumping along the rocky cliff wall.
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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".
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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.
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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.
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Judging by the way Virgil mounts the helmet and starts breathing immediately, the divers are breathing standard air. However, at that depth (2000ft) air would be instantly fatal, due to oxygen toxicity - not to mention completely impaired by nitrogen narcosis.
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The divers are supposed to be at 2000ft, however this is twice the depth of the ever recorded using open-circuit scuba equipment, something that took weeks of planning, a large team of support divers, and caused severe HPNS (High Pressure Nervous Syndrome) in the diver.
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The film's ending hinges on the fact that the protagonist is unable to distinguish "the blue wire with a white stripe" from "the black wire with a yellow stripe" (under yellow light). Basic industrial design guidelines would never have allowed this situation to happen. The reason why some wires are striped and some are not is precisely to make them distinguishable under colored lighting. In a situation like the one in the film, one wire would be striped while the other would be plain.
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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.
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Deep Core heating system should be damaged after losing the umbilical cable. Yet when Bud emerges from the moon pool, even though he is clearly freezing, his warm breath is not visible as it should be.
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Incorrectly regarded as goofs 

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.
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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.
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Revealing mistakes 

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.
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The steel pipes that Coffey reaches behind to get a duffel bag full of guns shift as he brushes them with his shoulder.
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When the men hanging on the subs jump off to investigate the nuclear submarine, a camera shot pointing upwards reveals the surface of the tank they were filming in.
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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.
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Water dripping from the control room ceiling in the Montana falls perpendicular within the camera frame instead of falling at an angle while the boat sinks.
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When Coffey runs into the water tentacle and freaks out (just before he closes the door on it), the camera pulls back into a wide shot that shows the base of the tentacle coming out of the pool. You can easily see where the real water ends and the CGI begins as there's a seam clearly visible.
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When Bud and Jammer first enter the Montana, a corpse floating in the foreground clearly blinks his eyes.
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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.
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After Hippy discovers Coffey and his partner working on the nuclear weapon, he inserts a tape into a VCR and begins recording. Yet, on the tape, when he plays it back for Bud, it reveals what Hippy was witnessing before he inserted the tape - what we, the audience saw along with Big Geek before he started recording.
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Spoilers 

The goofs below may give away important plot points.

Continuity 

Near the end of the picture, the alien "city" rises to the surface, carrying with it several sunken vessels along with the underwater rig. This of course implies that the vessels and rig were floating above the alien city as it rose from the depths. However, the rig was resting on a cliff edge and therefore could not have been lifted from beneath.
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Revealing mistakes 

Near the end of the picture, the alien "city" rises to the surface, carrying with it several sunken vessels. One of the ships, a freighter, is lying on its side with one of its propellers flexing and flopping from the wind (the ship, of course, is a model).
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