Six Forgotten Warriors Chapter 4: The Six Fight Again - S5-E5
Factual error: When Kingpin has Robbie dangling from a helicopter, Spider-Man jumps onto the helicopter and tells Kingpin he promised to release Robbie, to which Kingpin replies sardonically with "And so I shall." Neither of these two should be able to hear each other over the helicopter rotors. Spider-Man doesn't possess super hearing and Kingpin is a normal human.
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Plot hole: This series is in the same continuity as the other Marvel animated series from around the same time - X-Men, The Incredible Hulk, Iron Man, and Fantastic Four - by virtue of each aforementioned show crossing over with at least one of the others. This episode, which originally aired on October 17, 1997, establishes that Captain America had spent the last 50 years locked in another dimension with Red Skull, and the episode ends with he and Red Skull once again becoming trapped in the aforementioned dimension. However, the final episode of Fantastic Four, entitled "Doomsday," which originally aired on February 24, 1996, features a cameo by Captain America in the present day, attempting to stop a rampaging Dr. Doom.
Spider Wars, Chapter 2: Farewell Spider-Man - S5-E13
Revealing mistake: When Spider-Man is web-slinging with Stan Lee, they pass the same group of buildings twice, revealing it to be recycled animation.
Spider Wars, Chapter 2: Farewell Spider-Man - S5-E13
Continuity mistake: When Spider-Carnage has Gwen Stacy hostage, she is bound by portions of his symbiote. When Spider-Man frees her, she is suddenly bound by webbing instead of the symbiote.
Spider Wars, Chapter 2: Farewell Spider-Man - S5-E13
Continuity mistake: When Scarlet Spider is saying that they need to destroy the bomb, you can see one of the arms and tattered costume of the Man-Spider behind him, even though the Beyonder had already teleported Man-Spider to another dimension. It appears to be a shot from Spider-Man and Scarlet Spider's fight with Man-Spider that wasn't used and ended up being repurposed, rather than taking the time to animate a new shot altogether.
Spider Wars, Chapter 1: I Really, Really Hate Clones - S5-E12
Continuity mistake: When the group of Spider-Men are observing the Green Goblin and the Kingpin's henchmen from inside the ventilation shaft, the outside edge of the shaft cover is first shown to be on the wall outside of the shaft, and then inside the shaft itself when the Armored Spider-Man pulls the cover off.
Secret Wars, Chapter 3: Doom - S5-E11
Continuity mistake: After the Beyonder ends the war, he teleports everyone to a floating chess board in space, with Dr. Doom lying near the edge. When the shot changes, Doom has moved closer to the middle of the board. He is unconscious so he couldn't have moved.
Secret Wars, Chapter 3: Doom - S5-E11
Audio problem: When the Lizard says "Yes, Spider-Man," his mouth is wide open and motionless.
Secret Wars, Chapter 3: Doom - S5-E11
Revealing mistake: After Dr. Doom has stolen the Beyonder's powers, he demonstrates the powers to Ben Grimm in his throne room by teleporting Red Skull, Dr. Octopus and Smythe off the planet. Next he teleports all the heroes to his throne room, and the shot of all the heroes is from two episodes prior when all the heroes were battling the Lizard. This shot of the heroes also includes Ben Grimm in form as the Thing, meaning Ben Grimm was in two places at once. Spider-Man, the Lizard and the rest of the Fantastic 4 were also already prisoners in Doom's castle, which means they were all in two places at once as well.
Secret Wars, Chapter 1: Arrival - S5-E9
Other mistake: When Spider-Man is scrolling through his options of which member of the X-Men that he can teleport to the planet, the picture of Cyclops shows part of his yellow "bandolier" colored blue.
Secret Wars, Chapter 1: Arrival - S5-E9
Continuity mistake: Towards the end of the episode, Captain America stands up to pledge his support to Spider-Man. When the shot changes, Cap is suddenly sitting down. When the shot changes again, Cap is standing up.
The Return of Hydro-Man: Part 1 - S5-E7
Other mistake: When Spider-Man catches up to Mary Jane and Hydro-Man at the foundry, he webs up Hydro-Man's left wrist. When the shot changes to Spider-Man landing, he is not holding onto the web-line. When the shot changes back to Hydro-Man, his arm his pulled with the web-line remaining taut, even though Spider-Man is not holding the web. If Hydro-Man was moving his arm on his own, then the web-line would be slack.
The Return of Hydro-Man: Part 1 - S5-E7
Continuity mistake: When Mary Jane is hiding from Hydro-Man behind the barrels, one shot shows her bare arm under her yellow sweater, when the sleeves of her purple turtleneck that she wears under the sweater should be visible.
The Return of Hydro-Man: Part 1 - S5-E7
Other mistake: When Spider-Man breaks the chain off the steering wheel of the boat, several of the links on the back loop of the chain break off, which would be impossible since he broke the chain at the front.
The Return of Hydro-Man: Part 1 - S5-E7
Continuity mistake: When Spider-Man is in the lab analyzing Mary Jane's jacket for clues, the inside of the door to to the lab has the door knob on the right side. When Debra Whitman is trying to get in the lab, the door knob on the outside of the door is on the right side as well, when it should be on the left side. The inside knob also disappears when the security guards break the door down.
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Continuity mistake: When Captain America and Red Skull are grappling near the vortex, their fingers are interlocked. When the shot changes, their hands are pushing against each other's torsos.
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Other mistake: Two scenes in this episode are shown out of order. First we see Captain America and Spider-Man lying on the ground near the dimensional vortex at the mercy of Chameleon and the Red Skull, with Cap flicking a rock across the room to distract Chameleon so that he and Spider-Man can re-engage them in battle. Shortly after, we see Spidey and Cap arriving at the dimensional vortex to configure it to defeat Electro, with Chameleon and Red Skull attacking them once Spidey has finished with the vortex, revealing they had been lying in wait knowing full well someone would figure out that the vortex was the key to stopping Electro.
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Continuity mistake: When Captain America is giving Spider-Man moral support after Mary Jane's accident on the roof, the red glove on his right hand briefly turns blue when he puts his hand on Spider-Man's shoulder.
Six Forgotten Warriors Chapter 5: The Price of Heroism - S5-E6
Other mistake: When Spider-Man and Silver Sable are chasing the Red Skull and Kragov, they are able to deduce which direction they are going by identifying their footprints. However, Spidey and Silver Sable themselves don't leave footprints when walking over the same spot.
Six Forgotten Warriors Chapter 4: The Six Fight Again - S5-E5
Character mistake: When the Red Skull reemerges from the vortex, he sees Chameleon and acknowledges him as his stepson. However, only moments before this, Kragov explicitly stated that the Chameleon was more like an adopted son to the Red Skull.
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.