Factual error: The final dogfight scene has a huge error when Hollywood's jet is hit with a missile and he ejects. The next scene shows him manually deploying a small pilot chute to open his main parachute. After seat/man seperation, the main chute automatically deploys depending on altitude and airspeed. He would still be connected to his ejection seat until his chute deploys. Having to manually throw a "pilot chute" to the wind would leave too much for human error.
Factual error: When Goose takes the photo of the MIG's cockpit, the type of Polaroid camera he is using has an acoustic auto-focus system. It will not focus beyond clear glass or plastic because the ultrasonic pulse bounces off the glass and not off whatever is behind it. Therefore the photo would be focused on Goose's own canopy and the MIG's cockpit instruments (of interest to Charlie) would be very blurry. Perhaps that is why the photo is not shown. Also: Goose proclaims the photo great immediately after it comes out of the camera. In fact it takes a minute or so to develop and become visible.
Factual error: The beginning of the movie when Maverick inverts and gets cozy (canopy to canopy) with the MIG pilot and Goose is taking pictures could never have happened. The tails of the F-14 are nearly 9 feet tall and the canopies are a mere three feet apart, so this would have resulted in a collision.
Continuity mistake: The weapons armament on the F-14's keeps changing from one cut to another.
Factual error: When Top Gun first came out, everybody in our squadron made a big joke of the "Deadly Blue Tubes." This refers to the sidewinder missiles that were supposedly launched from the Tomcats. Those who are familiar with aircraft weapons, would know that the blue tube is a sidewinder simulator. If you were to launch this from the aircraft, all it could do is drop like a rock.
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)
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.
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.
Audio problem: Reference the dialogue in the hangar where Mav/Goose and Charlie are discussing what was happening when they met the MiG, and Goose says "You know, the finger." In the original 1985 cinema release, Charlie replies "Yes, I know the finger, Lieutenant," but in the video release this has been changed to "Yes, I know the finger, Goose." If you look closely you'll see that her lips don't move when she enunciates the word "Goose," and if you listen carefully you can hear the edit change in the soundtrack between "finger," and "Goose."
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.
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?