Factual error: Why did they send only one F/A-18 to look for the missing helicopter? There would usually be two - a lead and his wingman. I would have expected a Search-and-Rescue type or maybe even the U.S. Coast Guard.
Factual error: As Strannix and Krill walk down the "Broadway" passageway, they pass through several watertight doors. These doors never extend all the way to the deck, so anyone passing through one would need to exert some small effort to pick their feet up to step over the threshold. There is no evidence of this, and they continue walking through as if the deck were uninterrupted.
Factual error: In the last scene, where Chief Ryback is rendering honors to his deceased captain, he is in dress blues, with a gold crow. Since the movie takes place some 2 years after Panama, and Ryback received either non-judicial punishment or a Court Martial at that time for striking an officer, he would have lost his "good conduct" rating, and the crow would have been red.
Factual error: When the jet fighter is flying by the naval ship, it gets shot down by a CIWS Phalanx system. The control panel used to fire it is not the real control panel.
Factual error: The space amidships where the bad guys are supposed to be moving all those rails out doesn't really exist. Battleships were designed for compartmentation, with the largest interior spaces being the engine rooms. a space like that could fill with water and could easily cause stability problems. also, there was no provision for the 5 inch armor plate which comprises the deck above "broadway." A large open hole in this armor would have left the ship's machinery vulnerable to large caliber enemy fire.
Factual error: After taking the bridge and continuing down to kill the ranking officer, men are ordered to seal a door with a blow torch used for cutting metal, not welding.