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)
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. (00:29:10)
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: 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: After removing him from command, Ramsey reviews Hunter's record, which says that Hunter was last stationed on the USS Alaska, SSBN-723. The USS Alaska is actually SSBN-732. (01:00:50)
Continuity mistake: When the fat sailor gets on the bus, Dougherty is adjusting his hat with his left hand. In the very next shot he has his right hand on his hat. (00:11:45)
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)
Continuity mistake: When discussing the broken EAM, Hunter is holding the message with two hands or one hand depending on the angle. (00:53:50)
Continuity mistake: When Hunter is arguing with the captain, he is listing off points and raises his thumb and forefinger in points 1 and 2. When the shot changes, he has a closed fist. (00:57:00)
Answer: In a war situation, the Captain is absolutely NOT allowed to try and contact anyone, lest it gives their position away, which is why he was unable to question or confirm the order.
GalahadFairlight
All respect to GalahadFairlight, but Hunter was not asking the Captain to 'contact' anyone, but rather to use all possible measures to receive the EAM. Active contact was not required, and in fact, going shallow would have been 100% necessary just to launch the missiles, at which point VLF reception would have been easily possible. No nuclear submarine captain would ever have been so stubborn, nor so dismissive of his own XO. Both of these were pure Hollywood inventions.