Plot hole: When Terry gets back to her computer, after escaping from the spies and cops, the time is after 3pm New York time. If Jack actually is in Russia or Eastern Europe, wouldn't he have already gone to, and been killed at, that 5pm meeting?
Plot hole: Sarah breaks a mirror in frustration by throwing something against it. Then she buries her face in her arms and sobs. It remains a mystery how she managed to cut her hand so bad that it needed to be fixed with five stitches, as she isn't even seen picking up the pieces. (00:59:15)
Plot hole: In the debrief in Viper's office following Maverick and Goose's first flight at Top Gun (in which they defeat Jester), Viper states that "Commander Heatherly lost sight of you and called no joy." However, during the actual flight scene, you never hear Jester call "no joy." I've always assumed that this part of the scene was accidentally left in the editing room.
Plot hole: Near the end of the movie, when Packard is about to race the Turbo, he puts on a helmet. Where exactly did he keep this helmet? The '77 Corvette is a two-seater with very little storage space for the passengers. Oggie and Minty's helmets could have been in the back seats of their cars.
Plot hole: Chelsea says that when her deceased father gave her one of his paintings (now missing), he wrote an inscription to her on the back. She says she cannot prove that he actually did this other than he noted it in his journal and she does not know where the journal is. However, when Chelsea's father presented the painting to her on her 8th birthday, there were at least 100 adults present at her party who witnessed him giving her the painting, writing the inscription, and signing his name on the back of the canvas which was displayed to the guests. Any number of these people could be contacted and corroborate her claim.