Factual error: Every time one of the F-14 pilots fires a missile, he thumbs the selector switch on the stick to the SP/PH (Sparrow/Phoenix) position, then pulls the trigger. In every case, it's a Sidewinder that leaves the rail, even though it isn't selected, and would not have had time to "home" anyway.
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: 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: 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.
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.
Factual error: When Mav is talking to Charlie he said his dad went missing in an F4 in 1965. Much later when Mav is at Viper's house Viper states that he flew with Mav's dad in VF51. VF51 flew the F8 Crusader until 1971 when they transitioned to the F4, so if Mav's dad was in VF51 as implied in '65 he would have been in an F8, not an F4.
Factual error: Cougar would not have a photo of his wife and kids in the cockpit as seen in the opening scene, as it would fly around when maneuvering. It could also obscure instruments.
Factual error: In the final dogfight, it is declared that the MIG-28s carry the "Exocet" anti-ship missile. This missile is around 1,500lbs and would be visible on the enemy fighters. That additional wing loading would have made them ineffective in a dogfight and they would have been easily overwhelmed by the F-14s in a dogfighting (no external tanks or heavy ordinance) configuration. Not to mention that Exocet is a French-made missile and would not be carried by a Soviet fighter.
Factual error: The navy won't just allow anyone to pick their assignment, just for doing their job. Maybe if he had saved the president's life or something. He was not qualified to go back to be a top gun instructor. He barely graduated, he didn't win the trophy. He had tons of issues, and there there was not even an opening since neither of the current instructors retired. You can't just add a new instructor, they can only be replaced.
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.
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.