Quick glance at TV Tropes shows some issues, but nothing to sneeze at when compared to other films.

• Artistic License – Military:
• In real life, the command to launch nuclear weapons cannot be countermanded once confirmed, precisely because of what happens in the film. For that same reason, the Alabama would never have received a conditional order to launch at some indeterminate point in the future. Rather, they would have been directed to get into position, but the final order to launch would be withheld until the desired time. Though if they did that, there would be no story.
• Multiple members of the crew, including the command staff, are heavily overweight, in one arguable (and plot-relevant) case lethally so. While the Navy’s fitness standards aren’t extreme, they’re not that permissive.
• In the extended cut this issue is addressed in COB Walter’s case at least. Captain Ramsey asks Hunter to have a word with COB about his weight, rather than chastise a long-serving and faithful subordinate himself. During their talk COB acknowledges to Hunter that he’s overweight, then ruefully adds that he can’t seem to stop eating. Being on his last tour and an old shipmate of a legendary captain explains how COB has gotten away with his lax fitness standards.
• Zig-zagged in that the stereotype of chief petty officers (and senior and master chiefs) in the US Navy is that they are obese while chasing down their sailors about fitness standards, often to the ire of their juniors.
• Subverted in that a look around many modern navy bases reveals sailors who look roughly these sizes, and though they might be outside height and weight standards, they are being retained for their time in contract (while unpromotable) due to the need for bodies to fill boat seats. Additionally in 2024, the Navy removed the ability of commands to punish sailors directly for failing fitness tests, potentially exacerbating this issue. While it’s unclear if this body type was common in the 1990s, it’s certainly been common in the succeeding years.
• During the discussion on whether the Russians have already launched their missiles, Zimmer claims (in somewhat more colorful language) that one doesn’t prep nuclear missiles without the intent to immediately use them.note  This ignores the entirety of the Cold War, where both sides armed their missiles at various points but never used them.
• No captain, regardless of how well-respected they are, would ever be allowed to have a pet (least of all a dog) onboard their submarine.
• Running a weapons drill during an actual fire emergency is also a huge no-no.note 
• Though the Ohio-class is not nearly as cramped as older submarine models, it still does not have crawl spaces large enough for Hunter and co. to sneak around in.
• An SSBN would not be called upon to conduct the kind of nuclear strike the situation calls for, due to the very communications issue we see happen.
• As much of the film tries to present the situation as both sides having a point (including the final court martial), the reality is that Ramsey committed greater crimes for the sake of performing his assumed orders than Hunter did. Ramsey violates at least three articles of the Uniform Code of Military Justicenote ; Hunter, on the other hand, certainly didn’t threaten to kill anybody.
• American SLBMsnote  use solid fuels that do not require fuelingnote , but the fueling sequence allows for a better Race Against the Clock.
• Being unable to answer the question of who played the enemy commander in The Enemy Below is not an acceptable reason for pushups or punishment of any kind, and so Dougherty would be facing punishment himself. Superiors of any rank are never permitted to arbitrarily punish junior sailors with physical exercise such as a basic training drill instructor would do. This is considered abusive treatment, an illegal order, and the subordinate is not obligated to obey. Further, the officer can be reprimanded for misusing their authority.
• Picking Hunter as XO of a SSBN would not be by just the Captain through a simple interview, as implied in the film, but by a Navy board or even the SSBN squadron commander, senior to Captain Ramsey. It’s possible, though, that the “job interview” in the film is actually just Ramsey’s way of meeting his new XO before they serve together for the first time.
• Alabama is repeatedly referred to as a “ship”. US Navy nomenclature for submarines is “boat”.
• “Naval” is spelled as “Navel” in the title card for “U.S. Naval Headquarters Pearl Harbor” which is a spelling error usually reserved for double entendre jokes about the priorities of sailors in their free time.
• What’s another term for a lifeguard stand? A “navel” observatory.