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.
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.
The Wedding - S5-E1
Revealing mistake: After Scorpion causes the chandelier to fall onto Spider-Man, the camera pans to the right and Scorpion appears out of thin air onto the screen.