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.Jacob La Cour
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 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: 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: 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: 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: After the class where they meet Charlie for the first time, and Maverick reveals that he's "the one", he's confronted by Iceman. The Iceman asks him who was watching Cougar, while he was "show boating" with this MiG. If you watch Iceman you'll see that he puts his watch on twice.
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.