Continuity mistake: In the opening scene, we know Maverick and Goose are flying in the morning because the CAG is greeted with a "Good morning, sir" before he asks who is flying. As the scene plays out, it is certainly taking place during the day. However, by the time Maverick is escorting Cougar back to the ship, the sun is setting - by the time Cougar's plane lands on the ship, it is quite dark. First, it seems highly unlikely that the encounter with the MiGs would have taken that long, and the F-14's certainly wouldn't have been able to stay airborne that long without refuelling - which we never see.
Continuity mistake: In the first dogfight there are several shots where the planes are very close to the ground - especially one flying over a flat desert where you can see the planes' shadows. In those shots they are definitely below 10,000 feet. However it is only later said that they are going below the hard deck.
Continuity mistake: In the scene at the beginning of the movie when the Commander walks into the flight control room on the aircraft carrier and asks "Who's up there. Great Maverick and Goose"; he is only wearing pilot wings on his uniform. As the scene progresses when Maverick and Cougar tangle with the Migs, he is in the control room and his uniform changes to being completely decorated.
Continuity mistake: In the scene where Maverick and Slider are studying and Charlie slips Maverick the piece of paper with her address on it, Slider changes seats. First he is at one end of the table near the wall, then at the end of the scene he, and all of his stuff, is at the opposite end of the table.
Continuity mistake: In the scene where Kelly McGillis hands Tom Cruise the note saying "meet me at my house 5:30 sharp" or something like that, if you look carefully you can see when she hands Cruise the note that there is a lot of print on the sheet, but when he looks at it in a close up the sheet is totally white blank except for her writing.
Continuity mistake: Count the doors opening and closing - Mav walks through a closed elevator door.
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.
Continuity mistake: When the F14 lands in the opening scene, it is number 205. When it comes to a full stop, the number has changed to 114. (00:03:30)
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: While in the opening air scene, the names of the pilot and his RIO are backwards.