Plot hole: During the entire standoff between Blake & Travis, there is a Federation guard with his hands on his head. Yet when the scene first begins, no-one else is and Blake is not holding a weapon on anyone. Neither has he revealed his play with the virus at this point. After he has done so and left, the same guard still has his hands up. Finally, after Travis has secured the virus, the guard STILL has his hands up.
Other mistake: Just after Cally says that the pilot's death was "a misfortune," she stands and her chair scrapes noisily on the floor. The sound apparently startled Paul Darrow, causing the always-unflappable, nerves-of-steel Avon to flinch: the only time in all four seasons that he's ever seen, albeit briefly, to break character.