Factual error: Throughout the movie, all sorts of messages are passed over the 1MC (ship's intercom) when the boat is supposed to be stealthy. They've set "Ultra Quiet" to avoid the enemy sub but no-one was any quieter, and everyone was still using the 1MC. Worse, people are shouting commands and status updates, both in person, and over the intercom! No wonder that Akula found them. The only thing protecting this ship was plot armor! In real life, messages would be passed quietly using sound powered phones (which we also see), rather than blasting the info loudly to the entire crew, because sonar will literally pick up the sounds of loudspeakers and people shouting. Let's not even mention classified target data being passed to the entire ship's crew on the 1MC. (00:49:00)
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)
Factual error: Throughout the movie, everytime some type of casualty occurs or an alarm sounds, police type lights go off throughout the ship. Submarines don't have flashing lights or grated decks for that matter throughout the ship. The sound of the alarm is enough, since there are no deaf personnel on board a submarine. (00:23:10)
Factual error: Several times during the movie, we can see the radio operator with the screen contents "printed" on his face. As everyone knows, that just doesn't happen in real life. (00:25:00)
Factual error: After the 2nd sub attack, while Hunter is in charge, a call is made from conn to maneuvering, to restore propulsion as soon as possible. It shows a young black dude answering back on the MC, having to yell over the noise of water spraying everywhere. This was laughable. Maneuvering is the control room for the nuclear power plant. It's all control panels and 4 technicians plus the EOOW, a nuclear-trained officer or senior enlisted, who would be answering back to conn. There wouldn't be any flooding going on there. (01:09:45)
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.
Factual error: When the Captain (Gene Hackman) is getting ready to address the crew, the Chief of the Boat (an enlisted man) is briefly shown barking orders to the crew wearing a combination cover with an officer's golden chin strap. A Chief Petty Officer wears a black chin strap. Contrary to popular belief, it's not illegal to wear an accurate uniform on film, in fact the military offer their help to ensure uniforms are accurate: http://www.defenselink.mil/news/NewsArticle.aspx?ID=516, so that's not the reason. (00:15:41)
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)
Factual error: At one point, the US sub's starboard (right) side is shown to have an American flag painted on the hull near the bow. The flag's blue field is at top/left when on this side of any vehicle, it should be at top/right. Proper display of the flag requires the blue field always be located 'forward' of the remainder of the flag on all vehicles, be they plane, boat, tank or even space shuttle. (01:19:15)
Character mistake: When Denzel is talking to the crew about upgrading to DEFCON 3, they say the last time was 32 1/2 years ago during the Cuban missile crisis of October 1962. The problem is that they both take place during October, meaning that the half year part is a mistake. (00:34:00)
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)
Deliberate mistake: During the part of the movie where the USS Alabama is sinking deeper into the ocean a shot of the depth gauge was made showing the sub passing 1800 feet at a quick rate. About 20-30 seconds of shots were shown after this to further dramatize the peril of submarine and then the scene cut back to the depth gauge. This time however, the gauge was moving much slower and only shown the sub had sunk 15-20 more feet without any reason for the sudden slowdown in decent.
Character mistake: More than once the crew of the submarine salute the Captain while uncovered in the hallways of the sub. Sailors never salute without their cover on.
Factual error: Upon the order to dive the boat when leaving port, many of the crew are shown hurrying around (especially up and down ladders). Everyone would already have a place to be on the maneuvering watch.
Character mistake: At the end of the movie, Ramsey and Hunter begin a conversation about Lippizaner horses. Ramsey says they are from Portugal, Hunter says they are from Spain. However, the Lippizaner horse's place of origin is believed to be in modern day Slovenia (though they are believed to have descended from Spain in the distant past). Lippizan is Slovenia's national symbol. Plus Lippizans are associated with the ‘Spanish Riding school' but the ‘Spanish Riding School' is situated in Vienna, Austria.
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.