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)
Neogenic Nightmare Chapter 7: Enter the Punisher - S2-E7
Other mistake: Spider-Man and Detective Lee both comment on the skull on the Punisher's shirt when they first see him. However, the Punisher is wearing body armor that covers most of his chest and abdomen in this scene, so there's no way they would know that he has a skull on his shirt.