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.
Plot hole: Why was an F-18 even sent to look for the helicopter anyway? Krill was the only one on the ship at the time that knew who was really on the chopper, the crew only knew about Jordan Tate, and the captain believes it's supposed to be a surprise for him so he's not calling anyone, so who sent the F-18?
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.
Continuity mistake: During the final fight scene where Lee dies, Segal pushes his thumb into Lee's eye. If you pause the tape, you can clearly see Segal's thumb is bent inward.
Character mistake: When Rybeck gives Miss July basic instructions about the use of an Heckler & Koch MP 5, he calls it an assault rifle. This weapon is classified as a submachine gun (a machine gun firing a sub-caliber round). Someone with his training would know the difference.
Plot hole: When Ryback calls in to Admiral Bates and his people the first time he gives the size of the terrorist force at about 30. Now Ryback may be a badass SEAL but he is definitely not the best with numbers. 30 people including Krill would not be enough at all to run the operations of the ship including running the bridge, cutting the pieces necessary for the crane, running the engine room, not to mention all the people patrolling the ship that are looking for him after he has already taken out at least 5 of their men. So if they're getting this plan done, they're doing it with a hell of a lot more than 30 people.
Plot hole: There appear to be way more terrorists that take over the ship over the course of the entire film (if including all the different scenes) than what appears to have been able to fit on the helicopter (although Jordan mentioned it was full, the helicopter didn't look that big to hold everyone we see).
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.
Continuity mistake: Before Admiral Bates first speaks to Strannix, there is a dark-haired marine in a green uniform on his left. When Bates raises his hand to signal activating the audio to speak, Captain Garza (black uniform and silver hair) is suddenly on his left. Then it changes to another camera angle and the marine is back next to Bates. (00:36:40)jimba
Continuity mistake: When the helicopter lands we see it is sitting over the white circle of the landing zone on the back of the ship. Later, right after the F18 is shot down, we see an aerial view of the ship with a small part of the back cut off, but part of the landing zone circle is visible and there is no helicopter. (00:13:30 - 00:36:00)jimba