Sins of the Fathers Chapter 3: Attack of the Octobot - S3-E3
Factual error: When Spider-Man and Doc Ock are talking in the lab, at one point, a shot of Doc Ock's face shows Spider-Man reflected in each side of his sunglasses. However, Doc Ock's glasses have a singular lens, and the straight angle of Spider-Man's reflections suggest that the glasses are in no way curved, so Spider-Man should only be reflected in them once.
Sins of the Fathers Chapter 8: The Ultimate Slayer - S3-E8
Factual error: Despite being a paraplegic, when Smythe is about to be lowered into the vat of chemicals, his legs are pretty toned and muscular. The show implies that Smythe had been wheelchair-bound for a long time, so even if he had muscular legs prior to his paralysis, the muscles would have atrophied.
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.