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: 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: Before the final dogfight the horizontal stabilizer (back wings) on Mav's jet say YYY, afterwards they say XXX.
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.
Continuity mistake: The weapons armament on the F-14's keeps changing from one cut to another.