Plot hole: The Tomahawk Cruise Missiles the Arleigh-Burke Class destroyers carry have a range of approximately 1500km. As soon as Alex got the message from Sam, they could have blown that Saddle Ridge communications facility to kingdom come with just a few cruise missiles. They didn't need to get in range because the entire dome surrounding the Hawaiian Islands was smaller in diameter than the range of the Tomahawk Cruise Missiles. Cruise missiles have internal guidance, so they wouldn't rely on the radar, which was jammed.

Battleship (2012)
1 plot hole - chronological order
Directed by: Peter Berg
Starring: Liam Neeson, Alexander Skarsgard, Brooklyn Decker, Rihanna
Factual error: After the Missouri knocks the shield down, the admiral orders all aircraft launched, but the flight deck is shown in sailing transport mode, not flight readiness. It would have taken an hour or more to clear the deck and launch.
Admiral Shane: Prepare to fire.
Crew member: Sir, which weapons?
Admiral Shane: All of them.
Trivia: The missiles fired by the alien ships are the same shape as the pegs in the board game.
Question: In more than one scene, various officers are wearing some sort of necklace, apparently permissible additions to the uniform. They are of several different designs. What are they, and what do they represent?
Answer: They appear to be versions of a Hawaiian lei. During ceremonies and celebrations, it is permissible to wear pins, ribbons, and other items as a show of respect or support.
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Suggested correction: It's a non issue, it was a massive international naval exercise, Good chance of more than one carrier participating. In fact, every picture of an actual rimpac exercise has multiple carriers visible. Just because 1 carrier isn't in flight readiness mode doesn't mean that others aren't. Might explain why he ordered every plane in the air but there's what? Only 3 that actually save Mighty Mo.
True there may been more carriers but you are being attacked and invaded no flag officer would leave his deck cluttered they would be at battle stations for sure.
Blooddog35