Continuity mistake: The class at Top Gun was made up of the current best pilot/RIO air crews which had not previously attended the school, from various squadrons. At graduation, out of all the pilots in the Navy, including all the pilots from Maverick's squadron still on the carrier (some of which would have already graduated from Top Gun), Maverick, Iceman and Wolfman have to rush back to Maverick's aircraft carrier because they are the only pilots available that can go against the MiGs?
Continuity mistake: In the first dogfight, when Cougar freaks out he removes his face mask. When Maverick takes-off again to guide him down the shot shows Cougar and Merlin's plane from the side where Cougar is again wearing his mask. Then it cuts back to a face shot of Cougar and his mask is off again. (00:09:35 - 00:11:00)
Continuity mistake: Take notice of everyone's hands during the action sequences. No one is wearing gloves. As standard issue for military pilots, the gloves are made of Nomex and provide protection from fire and allow for a better grip when things get a little hot and heavy.
Continuity mistake: After the final dog fight where everybody is happily back on the aircraft carrier, Iceman exclaims: You can be my wingman anytime, and Maverick replies: Bullshit - you can be mine. Then they hug, and during that hug Iceman in someway manages to put his sunglasses on, from one cut to another
Continuity mistake: When the four pilots are playing volleyball, they have no sand sticking to them even though they are shirtless, sweating, and sometimes diving in the sand.
Continuity mistake: At the end of the briefing before the final scene, Iceman questions Maverick's capabilities. He's right to do so as Maverick can't make up his mind what aircraft he's supposed to be flying. First we see him climbing into the cockpit of an F-14, then when the aircraft is placed on the catapult, it changes to an A6 Intruder. When the order is given for Alert-5 launch, he's flying an F-14.
Continuity mistake: The flight where Goose dies begins over land - where the pilots are chatting. When they see the enemy they are over water. In the next shot they are over mountains and desert again, until they land on the water. That doesn't add up. There are no places in California where the desert goes all the way to the coast with no towns at all.
Continuity mistake: In the opening scenes of the movie, they show a number of planes landing and being prepped for takeoff. One of the planes landing has the number 114 clearly shown on the right side. This is Maverick and Goose's plane. Why is it landing when two minutes later they're on patrol 250 miles from the carrier?
Continuity mistake: Scene of Tom's last take off - the Tomcat's tail number changes before he lands OR TC changed planes mid-air.
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 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.