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)