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.
Corrected entry: A trained US Naval aviator would not pull up to get away from a rocket missile because a Surface to Air missile will climb at least twice as fast as the depicted non-supersonic jet fighter. (00:21:15 - 00:22:40)
Correction: The jet Burnett and Stackhouse are flying is an F/A 18 Hornet, a supersonic aircraft capable of pulling off the manoeuvre described in the mistake with ease.
Corrected entry: When Admiral Reigart is talking to Lt Burnett in his office about Burnett's resignation papers, they talk about being at war or not. The admiral says that they are always at war unless tied up in San Diego bay. No ship that size would be in San Diego bay. They are based in San Diego Harbor. This is not a mistake the admiral would make.
Correction: Via wikipedia: facilities in San Diego Bay are the only remaining major naval base facilities still in operation in the entire State of California.
Continuity mistake: In the scene where Burnett stops the Pickup truck and it skids. The blond haired passenger on the truckbed is leaning on the rail and suddenly on the next shot he is leaning on the truck cab. (01:03:00)
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.
Corrected entry: Early in the movie, when Gene Hackman is berating Owen Wilson for wanting to resign from the Navy, "Admiral" Hackman refers to the ship they are on as a boat. Not even an 18-year-old Seaman Apprentice fresh out of boot camp would make such a grievous error in basic naval terminology.
Correction: I'm in the Navy myself and people frequently refer to their ship as 'The Boat'. When my squadron deploys we all gripe about having to go back to 'The Boat.'
Correction: Any ship where a naval aviator has made an arrested landing on is called a "boat." The aviators have been saying this since the 1950s, because they know it annoys the rest of the crew.
Factual error: The two SAMs are shot 5 to 10 seconds apart. Yet the second SAM catches up to the first and begins to travel at the same speed. (00:18:40)
Plot hole: While parachuting from a shot down aircraft, why would a trained air force flight crew with a steerable parachute bypass the broad, open landing site to land in trees? (00:26:30)
Factual error: Gene Hackman is the Adriatic Fleet Admiral. While onboard the aircraft carrier, he carries out duties as the captain of the carrier. The only people who can give orders on a carrier are the ship's captain or the airwing captain. Gene Hackman could only give orders to the captain, who in turn would give orders to the crew.
Suggested correction: The mission was unsanctioned and off the books. So in this case where the Admiral was the one who went "rouge" to save his guy it's completely normal that he'd be giving direct orders. He would not funnel an order through a captain in an illegal operation.
Admirals can only give orders to the captain who in turn would give orders to the crew. Missions being unsanctioned and off the books, and the admiral going rouge to save his would not change that.