Audio problem: Just before midnight when the band is playing "Morning After" the camera pans out for a wide shot of the dance floor - the dancers are dancing MUCH too fast for such a slow song - and you do still hear the song.
Visible crew/equipment: When Rev. Scott swims up the first stairwell, after pushing aside the dead crew member, as his head comes up the shaft, you can see, very quickly, the flippers of a crewmember swimming out of the shot behind him.
Plot hole: Shortly after the ship flips over, the steward, Ackers, is asked why lights are on. He explains they are emergency lights that will last three hours. The lights are left on throughout the movie, but when they get out it is bright daylight. Considering the ship flipped at midnight, there is nowhere on any ocean where it gets light at 3:00 in the morning (03 hours after midnight).
Continuity mistake: When Gene Hackman shakes the metal doors that lead to the shaft, in a close-up he unlatches the small latch holding the doors together. After a cut showing some water filling up the passageway, it cuts back to the shaft where the metal doors are shaking, but the hook is now latched again.
Factual error: Throughout the end there is fire everywhere. All of that fire would consume any oxygen that was in the rooms and fill the rooms with heavy black smoke. They are walking and climbing everywhere without the effects that the smoke and lack of oxygen would have caused.
Revealing mistake: When the ship is upside-down and they're trying to get Susan down from the table, you can see that the table really isn't attached to the ceiling. You can see the center pool split into legs that are supposed to be connected to the floor, but when Susan moves around and shakes the table, the legs shake and you can see space between them and the floor. Even if the other legs outside of the shot were connected, the table would be leaning under Susan's weight.
Continuity mistake: In the scene where they start going through the pipe and end up in the funnel thing Gene Hackman takes off the pipe cover and leans it against the wall. After everybody gets into the funnel it shows the water lapping at the pipe. In the background you see the cover is leaning against the pipe, not the wall.
Continuity mistake: When Manny leaves Belle behind to join the others in the propeller shaft, a crew member is lying 'dead' behind him. As Manny passes him, you can see the crew member move his arm, possibly to get it away from the fire below him.
Continuity mistake: Just before Shelley Winters tries to persuade the others she should be first to swim the underwater corridor to the engine room because she used to be an underwater swimming champion, watch closely what she is doing with her hands in each shot before she speaks. In one shot she is fondling the medallion hanging on a chain around her neck; in cutaway shots you can see the medallion is hanging free and her hands are nowhere near it.
Continuity mistake: Just as Susan jumps down from the overturned table, you see a shot of her feet, and she is not wearing shoes. Then when she lands in the curtain, she has her shoes on.
Revealing mistake: During the dining room scene when everyone is eating. Look for the shot where Shelly Winters reaches over to Manny's plate, in the background you can see a boom mike.
Continuity mistake: When Gene Hackman is about to swim through the passage to the Engine Room, Red Buttons hands him a lit flashlight. The camera changes to Gene under the water, and he is turning on the light again.