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)
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.
Sins of the Fathers Chapter 7: The Man Without Fear - S3-E7
Continuity mistake: When talking with his father and Smythe, Richard Fisk's grey pants briefly turn into the same color as his suit jacket.
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.
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.
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.
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 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 9: The Haunting of Mary Jane - S4-E9
Continuity mistake: Mary Jane's gloves come and go when she's talking to Spider-Man on the rooftop at the end of the episode.
Partners in Danger Chapter 9: The Haunting of Mary Jane - S4-E9
Continuity mistake: Mary Jane's costume's gloves come and go between shots in Miranda's hideout.
Partners in Danger Chapter 9: The Haunting of Mary Jane - S4-E9
Continuity mistake: Miranda's pants legs go from both being torn to just the left one then the right one during her flashback.
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.
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.
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.
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.
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.
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.