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?
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).