Other mistake: When Stackhouse and Burnett are being chased by the SAM, they pull to the right after deploying flares and you hear a voice on the radio say "Chaff, Chaff, Chaff". Chaff is a cartridge of small metal strips released as a countermeasure for radar guided missiles. These small strips add noise to the radar and clutters it up giving the pilot about 5 seconds to evade the missile. Throughout the scene, several indicators such as the flares and exploding fuel tanks suggest that they are fleeing from a Heat-seeking missile, not a radar guided one. To add to this, the voice on the radio wasn't that of Stackhouse or Burnett and was added for radio effect.
Other mistake: At the very end, in the helicopter, Gene Hackman is wearing a full helmet with a mouthpiece so he could hear and talk to the people in the helicopter and back at the ship; Owen Wilson is not wearing a helmet or a mouthpiece. There is no way Owen Wilson could hear what Gene Hackman is saying and vice versa. Battle helicopters are very noisy; you must have a helmet to hear and a mouthpiece in order to speak to be heard.
Other mistake: When they show the Super Hornet ready to take off on the carrier we see lots of people standing around watching on the deck. The people are there because it is file footage of the aircraft's first carrier trials on the USS Harry S. Truman in 1998. As they bothered to CG paint over the trial markings on the plane, they could have erased the people at the same time.