Continuity mistake: In Niska's office, behind his desk, there is a door that slides open to a small torture chamber. In "War Stories," there is a small staircase that leads into this torture chamber behind the door. However, in "The Train Job" (the first time we see this chamber) there is no staircase.
Continuity mistake: In the scene where Malcolm Reynolds is being tortured, after Zoë takes Wash away, the villain cuts off Malcolm's left ear. The shot changes, and then returns to Malcolm, showing the other side of his face. Now the visible ear, the right one, is missing. The shot changes to the front, and now his left ear is missing again.