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)
Other mistake: Despite being in the same continuity as the 1992 X-Men animated series, this show depicts Bill Clinton as President of the United States, while in X-Men, the President is Robert Kelly.
The Return of Hydro-Man: Part 1 - S5-E7
Other mistake: When Spider-Man breaks the chain off the steering wheel of the boat, several of the links on the back loop of the chain break off, which would be impossible since he broke the chain at the front.