According to Miles Teller, the cast got to choose their own call signs. He chose "Rooster" because it was in the same family as "Goose."
The roof of the shack next to Ed Harris wasn't supposed to be lifted when Maverick flies past. However, they only had one chance to shoot it, so this was a very lucky occurrence. (As the Darkstar is only a non-flying mockup, the actual plane being used was cloned out and an image of the Darkstar was composited over it.)
The film is dedicated to the memory of original Top Gun (1986) director Tony Scott, who died by suicide on August 19, 2012 at age 68. He had been developing his own version of a sequel before his death.
The actors playing pilots not only had to film themselves, turning the camera on and off, they also had to touch up their own makeup, adjust their lighting, and handle their own sound. Sometimes, the director had to wait on the ground for hours for the actors to return with the footage. Adjustments would be made after viewing the footage, and the actors would have to go back up for another take.