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.
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: 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: 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.
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).
Factual error: In the scene where the ship encounters the tidal wave, the ship is located somewhere out in the middle of the ocean. A tidal wave would never break in the middle of the ocean. It's energy lies below the surface of the water. A wave needs to have land closer to the surface of the water for a wave to break, even if it is a tidal wave.