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: 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.
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.
Factual error: After the initial contact between the F-14 and the 'Soviet' MiGs, Maverick is on final approach and the LSO (Landing Signal Officer) instructs Maverick to 'Call the ball', referring to the ships 'meatball' landing light system. Maverick calls back 'I have the ball'. The correct phraseology would have been 'Tomcat ball' followed by fuel state, such as 5 point 5 meaning 5,500 lbs fuel remaining.
Continuity mistake: In the beginning scene of the movie, Maverick and Cougar encounter 2 Soviet Migs. When one of the MIgs is first shown from the camera angle on its right side, it is a delta winged aircraft. The next scene that shows the Migs, they have standard wings. The wings change at least twice during the opening air encounter.
Other mistake: The guy in the tower drinking coffee works at both Mirimar and the Enterprise? It is the same guy. Identical looking, hair color, wearing the same exact style of sun glasses, etc. The second scene, the air boss seems to refer to the first scene as well, making a statement of "g** d*** that guy!" and laughs after having spilled the coffee, as though this has happened before. Seems to me they are making it pretty clear its the same guy. I would think the air boss on a land based training facility would be a different person that the one assigned to the Enterprise.
Continuity mistake: In the final dogfight, Hollywood and Iceman are up against 5, count them, 5 Migs. Hollywood is shot down and Maverick is launched. Maverick takes out one Mig, Iceman takes out the next. That is two. Maverick takes out a third. For the finale, Maverick hits the brakes and lets him fly right by for a total of FOUR kills. Then the remaining Migs bug out. Two Migs are shown leaving. That adds up to 6 Migs, not 5. [Initially 5 Migs do show up on radar. But just after Maverick launches, Slider tells Iceman "We've got four on our tail. That makes 6 of them". So there isn't actually a continuity error when the remaining two Migs "bug out".]
Factual error: If a ship drifted into Russian waters, they wouldn't send for pilots that just graduated. They would use diplomacy first. They would send other ships and subs. They would only engage pilots if they were prepared to declare war. They would have hundreds of other pilots available. If any planes were shot down, it's an act of war. The two remaining MIGs would be joined by dozens more.