Continuity mistake: Count the doors opening and closing - Mav walks through a closed elevator door.
Continuity mistake: When Maverick goes to land while Cougar is in fuel trouble, the tailhook is down. He decides Cougar needs help and launches back off the carrier, the tailhook is up. The next view as he flies away from the carrier the tailhook is once again down.
Continuity mistake: At the beginning of the film, the squadron commander enters CATTC with a chest full of ribbons, next shot, all ribbons are gone. There is no smoking in CATTC (for the equipment) and the radar in CATTC cannot be used to monitor air combat movement as they did in the film. The Combat Centre or CIC is used for that.
Revealing mistake: The aircraft the American pilots are fighting against at the end are described as being "MiGs", but they are American F-5 jets, called Tigers, which the Navy is still using for the training of young pilots.
Factual error: In the final dogfight, it is declared that the MIG-28s carry the "Exocet" anti-ship missile. This missile is around 1,500lbs and would be visible on the enemy fighters. That additional wing loading would have made them ineffective in a dogfight and they would have been easily overwhelmed by the F-14s in a dogfighting (no external tanks or heavy ordinance) configuration. Not to mention that Exocet is a French-made missile and would not be carried by a Soviet fighter.
Suggested correction: The USS Stark was hit by Exocets. Wasn't flown by the French. The Exocet was/is used by dozens of nations (albeit nearly all Western-leaning). The adversary's nationality isn't specifically mentioned, intentionally, I'd bet. The aircraft markings suggest Soviet/Communist, but again, not mentioned.
Suggested correction: While it's mentioned they carry them, it doesn't mean they had to have them, but implies they could have them.
Continuity mistake: In the last dogfight, Ice says "two MiGs passing between us." It then shows the two passing between either Ice or Maverick and a single tail jet. The Grumman F-14 Tomcat is a twin tail.
Factual error: The navy won't just allow anyone to pick their assignment, just for doing their job. Maybe if he had saved the president's life or something. He was not qualified to go back to be a top gun instructor. He barely graduated, he didn't win the trophy. He had tons of issues, and there there was not even an opening since neither of the current instructors retired. You can't just add a new instructor, they can only be replaced.
Suggested correction: Take, for instance, the scene where Maverick goes into the flat spin; there are more than 2 A4s. Who is to say one of those instructors didn't leave, as they were never featured in the movie?
Continuity mistake: In the volleyball scene, Tom Cruise is shown oiled up, tanned, and with clear muscle definition. He then walks off the volleyball court in a new camera angle. He now does not have the muscle definition or neck area tan he had during the volleyball game seconds earlier. Additionally, the configuration and number of people in the stands is different from the previous camera angle.
Continuity mistake: Mav flies aircraft number 114 throughout the movie, then loses it in the flat spin. However when he is flying with Sundowner where he won't engage them in the final battle he is back in 114 again.
Continuity mistake: In the final battle scene, Slider sees two MIGs dead ahead and Iceman says he will "Take them down the left side." In a front view the two MIGs come towards them, but cut to a side view and the two MIGs pass, suddenly followed by a third.
Continuity mistake: The night before graduation, Maverick is parked on his bike at the runway. An incoming jet is seen, with gear and hook down. But in the next shot the jet just keeps flying. And it's not a test landing and take-off. It's two different planes mixed.
Continuity mistake: Towards the beginning of the movie Goose loses a bet to Maverick and must pay up. He extends his hand out with a bill folded. The camera switches back and forth and the bill changes from being folded in half to being folded in quarters.
Continuity mistake: While in the opening air scene, the names of the pilot and his RIO are backwards.
Continuity mistake: In the elevator scene Kelly McGillis's hair is a different colour (I think a shade of red) than earlier or later in the film. Apparently this scene was filmed months after Top Gun filming was complete while McGillis was shooting another film. This explains the baseball cap and ponytail.
Continuity mistake: When Charlie is briefing the pilots on what a MiG can do, Slider and the guy behind Maverick have their sunglasses on in one shot, then off in another and then on again in another.
Continuity mistake: In the scene where Charlie picked up Maverick from the hospital, you can see the rear view mirror of her car is low, between the actors' faces. The camera zooms in and the mirror can be seen raised slightly above the top of the windshield. The camera zooms out and the mirror is low again.
Plot hole: In the debrief in Viper's office following Maverick and Goose's first flight at Top Gun (in which they defeat Jester), Viper states that "Commander Heatherly lost sight of you and called no joy." However, during the actual flight scene, you never hear Jester call "no joy." I've always assumed that this part of the scene was accidentally left in the editing room.
Factual error: Maverick's total disregard to follow orders, land his plane when instructed too, plus his dangerous stunts while flying would immediately result in him being grounded, going before the naval board, and possibly having his flight status taken away for his disobedience. And he certainly wouldn't be chosen or invited to go to any TOP GUN school.
Other mistake: During the dog fight at the end the officer questions the status of Willard and Simpkin, previously designated the pilots on alert on catapults 3 & 4. The reply was "both catapults are broken". But carriers have four catapults - nobody even considers using nos. 1 or 2.
Character mistake: The Commanding Officer, CDR Metcalf (Viper), is wearing is CO pin under his ribbons on the left pocket. That means he used to be a CO, but is not currently. He should be wearing it over is right pocket to show that he is currently a commanding officer.