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.
Continuity mistake: Early in the film, a missile is fired from the ship, and it hits the satellite installation right outside the Navy headquarters (the people in the control room hear the explosion). It gets there very fast. Later in the film, a nuclear missile is sent towards Honolulu. That is supposed to take 24 minutes. Why so long, when the other missile got there much faster?