Sins of the Fathers Chapter 1: Doctor Strange - S3-E1
Continuity mistake: The hole in Dr. Strange's wall created by Baron Mordo's servants changes size and shape when Spider-Man is hanging Dr. Strange out the window. (00:10:25)
Sins of the Fathers Chapter 1: Doctor Strange - S3-E1
Continuity mistake: When Peter wakes up from Baron Mordo's illusion, he is wearing a monk's robe with sneakers and is barehanded. He removes the robe, revealing he was wearing his Spider-Man costume underneath, but his gloves and boots magically appear on his hands and feet as well. (00:09:45)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When the paramedics arrive to help Landon, they are shown approaching him from the direction his head is pointed. When the shot changes, they are now coming from the direction where his feet are pointed. (00:18:30)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: After Wolverine is knocked unconscious by the voltage of the cage that Beast is trapped in, Beast is able to keep Wolverine from falling into the vat of chemicals below the cage by gripping the fabric of Wolverine's costume. Once the fabric tears away, Beast is able to grab Wolverine by the hand. Once he loses grip, Wolverine is able to grab onto the cage itself. When Genevieve starts shooting the laser gun at the Hobgoblin, Beast is again shown to be holding Wolverine by the fabric of his costume. (00:08:30 - 00:12:05)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When the Hobgoblin crashes his glider into the railing, the entire glider is outside the railing's crossbar. When the shot changes, the glider is suddenly stuck between the gaps in the railing. (00:11:10)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: The size of the hole that Wolverine climbs through increases drastically. (00:07:45)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When Spider-Man says "I get the picture, Wolvie," he is shown to be running. When the shot changes, he is walking. (00:04:05)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When the targeting missiles lock onto Spider-Man, he is perched on a wall. When the shot changes, he is crouching on the ground. (00:03:05)
Neogenic Nightmare Chapter 4: The Mutant Agenda - S2-E4
Continuity mistake: When Spider-Man is battling the X-Men, he shoots webs at all of them, which they remove. Later when Spider-Man is in Xavier's study with the X-Men, Gambit is shown removing a piece of webbing from his right arm, even though he had already removed it earlier. (00:02:15 - 00:04:30)
Neogenic Nightmare Chapter 5: Mutants Revenge - S2-E5
Continuity mistake: When Beast is holding Wolverine above the vat of chemicals, the way they are gripping hands alternates between Wolverine gripping Beast's closed fist and their thumbs overlapping each others' knuckles. (00:11:00)
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.
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.
Continuity mistake: Kraven's arm band that he wears on his upper right arm switches to his left one briefly after he fights Spider-Man for the first time.
The Menace of Mysterio - S1-E5
Continuity mistake: Mysterio sounds cold and calculating in this episode. Yet in later ones he sounds different despite being voiced by the same actor.
The Sting of the Scorpion - S1-E6
Continuity mistake: The Scorpion gets bigger here, his eyes turn yellow, he gets fangs, his skin becomes sickly looking, and his fingertips resemble claws. Yet later on in later episodes he's missing all of that.
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.
Doctor Octopus: Armed and Dangerous - S1-E4
Continuity mistake: Doc Ock's left glove briefly disappears during his second fight with Spider-Man, and Jameson's pants are briefly his jacket's color during that fight.
The Menace of Mysterio - S1-E5
Continuity mistake: When Mysterio's unconscious he's in his costume. When Spider-Man leaves him webbed up he's wearing street clothes. But when he's shown on the headlines of the Daily Bugle he's back in his Mysterio costume.
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.