Sins of the Fathers Chapter 6: Framed - S3-E6
Plot hole: After Peter Parker is framed and arrested for selling government secrets to foreign organizations, he escapes police custody and goes home to retrieve his Spider-Man costume that was simply hanging in his dark room. If he was arrested for selling government secrets then surely the police would have searched his home and found his costume (as well as equipment) in the process. Since the police car was visible in front of his house, it seems very strange that police didn't search his home.
Plot hole: When Frankie tries to get Johnny to chase her out into space, he tells her he can't follow and warns her to turn back due to the thin atmosphere not being able to keep their flame powers active, and indeed her flames die out, and she begins falling back to Earth. However, several minutes later in the episode, both of them are just outside of the Earth when Terrax arrives, and again at the end after she becomes the new herald of Galactus, Johnny follows her into space well beyond Earth before his flames die out. (00:03:15 - 00:06:03)