Factual error: Throughout the combat sequences with the Russian submarine, both the enemy sub and the missiles exchanged between the USS Alabama and the Russian sub are shown as blips on a radar scope. In real life, sonar displays look much different and resemble a "waterfall" pattern that trained sonar specialists can read.
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.
Revealing mistake: After the XO orders all stop, we see a close-up of the ship's yoke being pulled back. The next wide shot shows the interior as the bow of the sub is rising, and just before this shot ends, note the console that the man with headphones is working at. A pair of crewmembers cross paths in the foreground, then the entire console wobbles, proving it isn't attached to the floor at all. (01:09:00)
Continuity mistake: When Denzel Washington meets Gene Hackman for the first time, Hackman is holding a cigar in front of his mouth. In the next shot, his arm is suddenly down on the table, and he lifts the cigar to his mouth again. (00:06:30)
Chosen answer: The ship has a second antenna, but the radio is damaged during the torpedo attack. Therefore they have to fix it in order to use the backup antenna.