Other mistake: At the beginning of the episode, Abby is almost run over by a man driving an SUV. They exchange words and then Abby throws a supposedly full cup of coffee at him. The cup of coffee bounces off the seat of the man's car and it is obvious that the cup is empty.
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)