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.
Sins of the Fathers Chapter 7: The Man Without Fear - S3-E7
Plot hole: They forgot Daredevil can sense when someone's lying, one of his powers. So, he should've known Spider-Man was telling him the truth about the computer disk.
Answer: Yes. Many things that would have been in the sixth season would have had Norman Osborne returning from limbo and reclaiming the title of the Green Goblin, Richard Fisk, the son of "The Kingpin" Wilson Fisk would return as a crime lord known as "The Rose", Ghost Rider would have appeared to help Spider-Man stop Dormammu from returning to Earth and Madame Web and Spider-Man would rescue Mary Jane from limbo.