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.
Factual error: Iceman is hit by cannon fire and has to shut down the right engine as a consequence. Later on, when Iceman and Maverick return to the carrier, Maverick asks for a flyby, which both tomcats perform as if nothing had happened to Iceman's plane. This violates regulation, essential safety protocols and it contradicts both Maverick and Iceman's personalities. The first thing you want to do when flying with only one engine (because your plane is damaged) is to make sure you land as soon as possible, you don't perform flybys, you don't even consider it. The remaining engine could fail too, turning the tomcat into a glider, that would mean the loss of the plane and it would put the lives of both pilots at even more risk. Maverick wouldn't allow this after losing Goose and Iceman has that nickname and reputation because he's a perfectionist, he plays utterly by the rules he wouldn't act like a fool when flying a damaged plane in that context. Also, Iceman performs that flyby with both engines running, which is absurd. (01:39:20 - 01:40:00)
Factual error: Although it doesn't occur in the land-based tower at Miramar during Mitchell's first high-speed pass (thankfully), when he repeats the pass at the carrier, the camera work tries to make it look like the jet rocks the tower. US super carriers displace over 100,000 tons, and are not pushed around even by 30,000 pounds of thrust flying nearby.
Factual error: The implausibility of holding class in a hangar instead of a classroom has already been mentioned. But how about the desk just inside of the hangar doors, complete with blotter, "in" and "out" baskets and other accessories?
Factual error: When Mav explains to Charlie his dogfight with the MiG-28, Charlie asks him: "You were in a 4G inverted dive with a MiG-28?", "Yes Ma'am" he replies. Imagine the two aircraft. The F-14 was inverted (the back of the F-14 was "looking" at the ground, and it was pulling 4 positive G's), and the MiG-28 was flying horizontally (belly of the MiG-28 was "looking" at the ground) so it should have been pulling 4 negative G's to keep their distance constant, or more to increase it (otherwise they'd have collided). For the MiG to pull 4 negative G's is almost impossible for two reasons: 1) the negative g-limits of the aircraft are somewhere in the area of 3.5, and 2) the Russian pilot's eyes would have popped out of his head at this g-force. Even the most modern and agile fighter aircraft of the world (like the F-16 and the Eurofighter) have a negative g-limit of 3.5 while their positive limit is at 9, mainly due to human body constraints.
Factual error: In the final dogfight scene, the Search and Rescue helicopter lands with rescued pilots very soon after the last F-14 lands. The dogfight took place approximately 250 miles away from the ship. The top speed of an H-3 is 120 knots. It should have taken the helo nearly two hours to return to the ship.
Factual error: US Flight suits certainly have their share of insignia on them, including name, rank, unit and sometimes others. Often aircraft type, school and hours awards are also worn, but they don't look as much like NASCAR fire suits as the movie makes out. Even so, all extraneous insignia are removed when operating in a combat zone. They're attached with velcro for this purpose.
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.
Deliberate mistake: In the locker room scene after the final dogfight, Wolfman's helmet is seen hanging in Hollywood's locker. Hollywood's helmet is blue. (01:42:15)
Factual error: After the final dogfight scene when Maverick and Iceman have landed, we see their two F-14 Tomcats spotted (parked) on the flight deck of the carrier. In the background, you see aircraft already spotted on the fantail (back of the ship) with several blocking the direct path of any aircraft landing on the carrier. While the aircraft directors and blueshirt crews would be fast in moving aircraft, they would not have had the time to spot and tie down all those aircraft on the fantail before Maverick and Iceman had finished parking their jets.
Factual error: After the graduation at Top Gun, the next scene shown is an aircraft carrier and the caption "24 hours later." To allow pilots time to overcome the effects of jet lag, they are grounded one day for every three times zones they crossed. Maverick wouldn't even have been on the flight schedule within 24 hours of having left California.
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.