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.
Deliberate mistake: Charlie is chasing Maverick in her car to tell him how she feels. Maverick races down the road on his motorcycle, then two cars start to move out of an intersecting road and Charlie narrowly misses them. In the next shot, Maverick starts yelling at Charlie about her 'reckless' driving, but behind them, you see the highway, with no traffic lights or signals. Charlie actually had right of way.
Deliberate mistake: At the beginning of the movie, during the first encounter with the Migs, Goose whips out a Polaroid camera and takes a picture of the Mig while inverted. There is no chance that the other plane would be visible in the photo. Goose used a flash bulb. The glass of the canopy would reflect the majority of that flash right back at the camera. The only thing that would appear in the photo would be a big white flash of light.