Factual error: In all sequences where Maverick "puts on the brakes", he is shown pushing the throttle quadrant forward and pulling the stick back. This would put him in a full-afterburner climb, but you don't really stop and it doesn't work in a medium speed tail chase (which is easier to film). The air brake does effectively nothing on the F-14 because it is too small, and not deployable at full power.
Continuity mistake: Before the final dogfight the horizontal stabilizer (back wings) on Mav's jet say YYY, afterwards they say XXX.
Character mistake: In the opening scene is a paragraph describing why the Top Gun school was started. The word "insure" is used when the word should have been "ensure". They wanted to guarantee the U.S. had superior pilots, not take out an insurance policy.
Continuity mistake: After the final dogfight, how did the drop tanks get back onto the planes before they landed? They sure weren't there during the dogfight.
Factual error: All the scenes with actors in the cockpit were shot in the front cockpit. Pay attention to the canopy frame behind the RIO. This would also explain a large gaffe from the movie - Merlin taps on the fuel quantity indicator and exclaims "C'mon Cougar, we gotta land this thing, we are way low on gas." The particular fuel quantity indicator shown being tapped by 'Merlin' the RIO, the one with the vertical tapes, is present only in the pilot cockpit. The F-14A rear cockpit has only a small fuel totalizer.
Factual error: Just as Mav goes into the flat spin, you hear a voice over while looking at the rear of his F-14 (you can see the AB), you hear "Engine 1 is out" and you see the right engine flame out... this is engine 2, engine 1 is the left engine.
Factual error: During the briefing before the final scene, the Commander says, "The Migs carry the Exocet missile. They can fire that missile from a hundred miles away." Yes they could fire the Exocet from a hundred miles away, but the Exocet's maximum range at the time of this movie was around 40 miles. Plus the Exocet is a French missile and would not be on a Soviet Union fighter.
Deliberate mistake: In the shot where the F-14 and F5 canopies are only 3-feet apart, you can see that the writing on the side of MAVs F-14 is backwards. Also, if the F-14 was inverted, with the sun more-or-less above, its cockpit would be in shadow, not with sunlight on the nose, as seen. (00:08:55)
Continuity mistake: The weapons armament on the F-14's keeps changing from one cut to another.
Factual error: This is the most basic mistake of all, but probably only obvious to those who fly in the Navy. Almost every written reference to "TOP GUN" is wrong. TOPGUN is one word, all caps, always has been.
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.