Other mistake: I don't remember there ever being an Alert 5 aircraft during normal flight operations, like Maverick was at the end of the movie. He should have been up in the air already. The Alert aircraft were normally set up before normal flight operations started in the morning.
Add timeKen Hogan
Other mistake: When Maverick goes to Charlie's house for dinner the first time, you see the "For Rent" sign in front of the house. At this time, she has said that she's only applied for another position. Much later, after Charlie and Maverick talk about her actually getting the promotion, he drives by her house on his motorcycle and seems to focus on the presence of the "For Rent" sign out front.