Other mistake: In the Darkstar takeoff sequence, there is a cockpit shot where Maverick looks back after passing over the Admiral, then looks forward into the cockpit. You can see that the landing gear handle is still in the "down" position and the 3 "gear down and locked" lights are illuminated. At this point in the flight the gear has already been retracted (confirmed visually in the previous external shot).
Other mistake: The film's premise is attacking a target that GPS jamming protects. As the attack starts, it is becomes apparent that no such protection is in place. GPS jamming is a form of radio frequency jamming. It would severely affect all radio communications. But planes and their command carrier are in constant, undeterred radio contact. Moreover, the enemy uses radar-guided SA-3 Goa SAM units that would have been unable to operate properly in jamming conditions.
Suggested correction: GPS jamming is transmitting radio signals on GPS frequencies, not all radio frequencies. It might prevent GPS being used for navigation or weapon aiming, but it would have little or no effect on radios or radar which use different frequency bands. At the risk of oversimplifying, it's like you could shine a bright flashlight to blind people trying to see you, but it wouldn't stop them using infra red (or hearing or smell or whatever else).
This correction is a mistake in itself. Without wide-spectrum jamming, the U.S. Navy never needed to use NAVFLIR for payload guidance. The site would be open to attacks from other radio-guided weapons, such as NAVCON guidance, standoff missile, and operator-guided bombs, especially since they were hard-pressed to guide their payload through a small window and ensure the survivability of their pilots.
In the movie they say GPS jamming, not wide spectrum jamming. GPS could be affected, but radar etc would still work. Like you say, the site would still be open to other attacks, and be able to use various defences.
It doesn't really matter. Maverick was told that GPS is jammed, so he threw all kinds of attack plans based on radio guidance out of the window, behaving as if there was a full-spectrum jamming in place. And his commanding officers didn't mind. Either the film's mistake is in its depiction of U.S. Navy's understanding of aerial warfare or its depictions of aerial warfare itself. There is huge mistake in there, it is only a matter of where.
Other mistake: When Cyclone and Warlock show Maverick the 12 candidates, Maverick looks at Rooster's profile, left of which is that of Hangman. There you see that Rooster and Hangman have the same Department of Defense ID: 720,956,349. (00:20:06)
Other mistake: After Hangman shoots down the last 5th Gen fighter you can see his F-18 in all remaining shots including landing still has all its missiles. (01:55:41 - 01:56:20)
Other mistake: In movie, Harvard and Yale are the crew of one of the dual F18. Harvard is wearing the Navy Aviator Wings on his patch, Yale is wearing WSO wings. Later, in aerial scenes, Yale is in the front seat of the plane and Harvard in the rear - the wrong way round. (01:40:00)
