Continuity mistake: When the F14 lands in the opening scene, it is number 205. When it comes to a full stop, the number has changed to 114. (00:03:30)
Continuity mistake: When we are first introduced to Maverick and Goose, their Tomcat crosses the screen, right to left, in close-up, slowly. It's nose is marked 203. Then we see the other Tomcat flying with them, and it is number 114, and its crew is Cougar and Merlin. But all the shots after this place Maverick and Goose in 114. (00:04:35)
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: In a scene soon after Cruise's partner dies, when he's flying with his new partner, you can see his call sign on his helmet, but when they get on the ground and he's talking to Cruise, all the letters on his helmet are removed.
Continuity mistake: The Navy allowed only two live missile shots (one AIM-9 Sidewinder and AIM-7 Sparrow) for the filming of the movie. Maybe that is why we see so many missiles fired from an empty rack.
Continuity mistake: Before the final dogfight the horizontal stabilizer (back wings) on Mav's jet say YYY, afterwards they say XXX.