Factual error: During the Recon flight launch, one shot shows the Super Hornet taking off with a blue Sidewinder. These blue missiles are simulation Sidewinders, and as stated in the Top Gun mistakes (same missiles used), all they do when launched is drop from the aircraft. (00:14:50)
Suggested correction: AIM-9 CATM's don't fall off the aircraft.
Other mistake: The Admiral gives Burnett a dressing down for his bar fight on Sept 23 and then a month later another complaint at a Chinese New Year party. This would mean the New Year was in October, but they are always in January or February. (00:10:00)

Continuity mistake: When Owen Wilson parachutes through the trees, his oxygen mask goes from being on, covering his face, to being off and dangling. This repeats when he drops from his tangled chute. When he initially cuts free, his mask is over his face, then when he gets up it is off. A pilot should keep his mask on and visor down after ejecting over land to prevent injuries to his face and eyes should he wind up in the trees like Wilson did. (00:24:40)
Factual error: Any satellite that could detect the scene where Owen Wilson is under a dead body, the satellite would be traveling so quickly it would be out of range in a handful of seconds - not minutes.
Continuity mistake: The SAM that's used to shot down the F-18 is a BRDM-2 mounted 9K31 Strela-1 which uses either 9M31 or 9M31M IR missiles. The missiles seen flying after the F-18 aren't either of those models. (00:18:40)

Visible crew/equipment: In several shots above Stackhouse and Burnett's plane you are able to see studio lights. (00:21:30)
Audio problem: When Burnett is running over the bridge yelling for the car his mouth doesn't move. (01:02:50)
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.
Revealing mistake: Towards the end of the movie when Burnett is by the plane's ejection seat, you see a puddle of water by him with snow flakes floating on top of the water. Snow flakes dissolve in water as soon as they hit. They use a corn starch type mixture to make fake snow, and that is what you are seeing in this scene.
Plot hole: When Burnett is hiding in the mass grave, the people on the ship are watching a thermal image of him. When he falls, his arm is at an angle and stays at that angle. To move under the bodies in the grave he would had to have moved his arm. But it stays at the same angle throughout, so how could he move under the bodies, without his thermal image moving? (00:42:00)

Revealing mistake: When Burnett stabs Sasha the sniper with the flare, you can see the outline of the padding visible under his blue jacket. (01:29:20)
Revealing mistake: When Owen Wilson is trying to restart the beacon in his ejection seat, his right hand is ungloved. Yet in the scene before, he took off his left glove. It is my belief the negative is reversed, as you can catch a quick view of a Duracell battery with the letters mirrored. (01:24:43)

Continuity mistake: The metal rod Burnett uses to stop himself from sliding down, while being shot at by the sniper, changes after he grabs it. (00:38:15)
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.
Continuity mistake: In the scene where Serbian soldiers are searching for Owen Wilson's character almost all of them following the tank in that shot are left-handed. A few minutes later it happens again. In all other scenes most every soldier is right-handed. The odd shots are flipped. (00:40:10)
Factual error: The heat seeking missiles would not have gone after the fire ball created by the fuel tanks as shown in the movie. Heat seeking missiles don't go after just any heat. They go after specific frequencies of infrared found in jet engines. (00:20:00)
Factual error: Fighter jets cannot dodge heat seekers head on. Missiles are simply too fast to be dodged head on by a jet due to the fact that fighter jets have to be at full throttle to stay in the air. (00:20:50)
Suggested correction: Actually they can. Head on presents less of thermal signature to the missile, as the aircraft engines are in the back. A radar guided missile could not be dodged so easily, however.