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.
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.
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: Pretty much everyone who fires a missile in this movie uses the stick's trigger. In a fighter aircraft, the trigger controls the radio/intercom or fires the gun. The red button on the far left fires weapons after the hat or castle switch selects them.