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 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.
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.