In the Shadow of Z'ha'dum - S2-E16
Other mistake: In this episode, a simple light frequency modulation enables Sheridan to briefly see the Shadow creatures. But because J. Michael Straczynski decided that this was just "too easy," the technique was "accidentally on purpose" forgotten about for subsequent episodes. If the Shadows had somehow learned to adapt and remain invisible, lines to this effect would have been written in. JMS deliberately chose to "conveniently forget" about it instead. (00:40:00)
The Origin of the Fantastic Four: Part 1 - S1-E1
Other mistake: When Puppet Master is making a clay figurine of Thing, the mold he uses doesn't have a Thing-shaped interior with which to make a detailed figurine. The figurine should have just looked like an undefined human-shaped figure. (00:15:20)
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.