Continuity mistake: During the opening sequences when the admirals are debating giving Dodge a command, Admiral Graham says that "three years ago" Dodge brushed up against a Soviet sub off Murmansk and that "as an ensign" Dodge got so drunk he ended up with his tattoo. Yet in two conversations with Lt. Lake Dodge says the tattoo came after the Murmansk incident.
Factual error: It is said in the film that the Stingray is a Balao class submarine. The Stingray was actually a Salmon class submarine, and likely called a Balao class because the USS Pampanito, which stood in for the Stingray in the film, was a Balao class. Source: http://uboat.net/allies/warships/ship/2938.html. (00:05:45)
Factual error: After the Stingray does the simulated attack in Charleston Harbor she launches a red flare. A green flare is used to indicate a "gotcha" in an exercise and would have been used there. A red flare indicates the submarine is in trouble and will attempt to surface.
Factual error: The uniform that LT Lake wears in the last scene is wrong. The Service Dress White Uniform for women includes a white shirt and black necktie. There is no way the Navy lets anyone walk around with visible cleavage. This has nothing to do with the myth that it's illegal to portray actual military uniforms, which is entirely untrue.
Plot hole: How did Admiral Graham know how the Stingray got past the Orlando in Charleston? Did Dodge tell the Admiral that they pretended to be a fishing boat on top of the water? Admiral Graham specifically stated that "the weather was the deciding factor." How would he know this unless he knew the exact tactics involved? Generally the weather doesn't affect the submarines underwater.
Character mistake: When Pascal gives his mutiny speech he refers to comsubpac, the Submarine Command for the Pacific fleet. He should have said comsublant. It seems to be a common theme of mistakes seeing as the museum sub they used for the Stingray is kept at a pier in San Francisco. Most of the scenes at dock are filmed there and at sea in nearby waters. Its possible that the original script was based on a west coast 'war game' and later got changed after a number of scenes were already filmed. (01:01:00)