Continuity mistake: When the incomplete second EAM is shown in the movie for the first time, its subject line states "nuclear missile launc..." However, when this same message is finally received at the end of the movie the subject line states: "terminate launch all missiles". If the first one had been consistent with the second this would have made quite a difference. (00:55:45 - 01:45:25)
Continuity mistake: After the submarine is hit by the first torpedo, all the crew are picking up things that have fallen down in the underwater turbulence. Then when the captain returns to his personal cabin, all his belongings (most noticeably on his desk) are all in position as though the attack never happened.
Continuity mistake: As the Alabama dives for the first time you will notice that the periscope and antennae masts protruding from her conning tower keep switching from up to down, indicating that the film crew used footage from two different sub dives to achieve that sequence. (00:18:50)
Continuity mistake: The captain says to make torpedo tubes 1 and 4 fully ready. When they're fired, they use torpedo tubes 2 and 4. (00:46:15)
Continuity mistake: In the scene where the "Alabama" dives, what we see isn't a ballistic missile-carrying submarine (SSBN), but an attack sub (SSN); actually more than just one, since the masts and periscopes keep going up and down in different shots. It seems that the navy wasn't too willing to cooperate in the production of a film depicting a mutiny onboard a nuclear sub, so the shots were "stolen" from a helicopter in the vicinity of some navy base.