Factual error: Shortly after our hero ejects you see the pilot flailing around trying to pull the ejection handle. In a Navy aircraft with two crew, the NATOPS manual (Naval Aviation Training and Operations Manual) clearly states that the seats must be set in the "command eject mode". This means, regardless of who initiates the ejection procedure, the rear seat goes first, followed by the pilot 1/2 later. There is no need for the pilot to pull the ejection handle.
Continuity mistake: After seeing his pilot get shot, Owen Wilson's character starts running uphill while being shot at. Of course you know he's being shot at because you can see the tracers. However, after cresting the hill, and starting down the other side, you STILL see rounds going past him. How did they get smart bullets?
Continuity mistake: The three Marine helicopters leaving the carrier are three UH1N Marine model helicopters. When they arrive in Bosnia to rescue the downed Navy pilot the same helicopters become two Bell model 205C and a Bell 412. When landing back on the carrier with the rescued pilot, they are again N models.
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.
Continuity mistake: Gene Hackman begins the movie as a two-star rear admiral. Later in the movie, however, shortly after the second stand-down ordered by NATO Admiral Piquet, he wears three stars on his collar, signifying a promotion to vice admiral. This is highly unlikely, as he spends nearly all of the movie in the grease with his superiors. By the end of the movie, he retires as an Admiral with 4 stars on his uniform.
Factual error: When the plane is called to shut down and abort, the crew leaves the aircraft and starts throwing the football around, but in real flight ops, a helicopter takes off first just in case an aircraft goes down. With that being said, the aircraft would have to taxi back to spot, and the helicopter would have to land. Everyone would still be in full flight deck gear.
Deliberate mistake: During the ejection sequence there is a major problem with the parachutes used by the crew. When you see the first parachute open, it is a standard Navy Conical round canopy with 3 colours; Orange, Green and White from the bottom view. A moment later they are flying ram air rectangular parachutes with different colour patterns.