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 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
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
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
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.
Partners in Danger Chapter 8: The Return of the Green Goblin - S4-E8
Continuity mistake: When the Green Goblin is first confronted by Spider-Man, he is riding his regular glider. Then after he pushes Spider-Man down onto the roof, one shot show him riding the larger glider.
Partners in Danger Chapter 6: The Awakening - S4-E6
Continuity mistake: When Morbius is battling Spider-Man and Black Cat on the rooftop, his red eyes are colored white in a couple of shots.
Partners in Danger Chapter 4: Return of Kraven - S4-E4
Continuity mistake: When Kraven is climbing the cage, it briefly changes color from silver to red.
Sins of the Fathers Chapter 3: Attack of the Octobot - S3-E3
Continuity mistake: When Doc Ock is being taken away in handcuffs at the end of the episode, his mechanical arms are missing. The arms were fused to his spine, so the police couldn't have confiscated them.
Sins of the Fathers Chapter 3: Attack of the Octobot - S3-E3
Continuity mistake: When Doc Ock is about to unmask Spider-Man in his lab, there is a brief shot of Doc Ock standing under a night sky. This is from their rooftop battle in the previous scene/episode.
Neogenic Nightmare Chapter 11: Tablet of Time - S2-E9
Continuity mistake: When Dr. Connors starts transforming into the Lizard after being blasted by the robot, the sleeve of his lab coat magically becomes tattered at the same time his hand transforms. Subsequent shots also alternate with his sleeve being tattered and pristine as well as his hand being reptilian and normal.
Partners in Danger Chapter 5: Partners - S4-E5
Continuity mistake: When Smythe is discussing his plan with the Silvermanes, his yellow eyes are blue in one shot.
Sins of the Fathers Chapter 11: Carnage - S3-E12
Continuity mistake: When Carnage escapes from prison a shot of venom escaping is used before changing back.
Continuity mistake: When Peter and Debra are approaching Dr. Connors' office, the nameplate on his door misspells his name as "DR. CURT CONNeRS". After they have entered the lab, the nameplate is shown to have the correct spelling. (00:06:10)
Sins of the Fathers Chapter 1: Doctor Strange - S3-E1
Continuity mistake: After Spider-Man, Mary Jane, Dr. Strange and Wong escape from Baron Mordo's lair, the lair itself disappears into thin air because of, according to Wong, the fluctuation of diminishing portal energy. When Spider-Man is saying farewell to Dr. Strange, the lair is there again. (00:18:30 - 00:19:05)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When Gambit waves to Beast after catching Genevieve, his gloves are missing. (00:16:55)
Neogenic Nightmare Chapter 4: The Mutant Agenda - S2-E4
Continuity mistake: When Professor X is explaining his line of work to Spider-Man, the neck portion of Gambit's headgear is flesh-colored. (00:04:35)
