Plot hole: When the Liberator returns to the planet, Travis remarks that their orbit is too far away to use their matter transmitter. Since Travis had only found out that they even HAD a matter transmitter (which the Federation hasn't managed to develop yet) when he spoke to a technician just before that, how would he know what the range was? (00:43:50)
Plot hole: Avon delivers his summation of the crimes and the murderer's identity to the Ortega's crew - with his back turned to the guilty party the entire time. This gives the killer ample time to pull a gun on them. But it's also egregiously out of character for Avon, whose suspicious nature bordered on paranoia and would never have allowed him to be so careless. (00:42:25)
Plot hole: Kendall stresses that only he can open the safe containing the valuable neutrotope. Yet later, he casually asks a crew member to retrieve it, with no mention of the safe's combination, making it a cinch for the villain to steal the goods and hand over an empty box. Naturally, no one bothers to look inside before Blake races off with the container. (00:16:30 - 00:21:05)
Plot hole: When the newly-acquired Orac is first set up on the flight deck, Blake comments that "the other end's connected." Connected to what? Orac didn't require plugging in, other than putting his activator key in place, and that was never connected to anything else. (00:46:45)
Plot hole: When he first shows the burned ison-crystal to Cally, Avon says that its loss will blind the Ortega's forward vision. Later, he assigns it a completely different function, saying it controls the hyperdrive instead. If this one little crystal is that vital to the ship's systems, why aren't these guys carrying a spare? (00:15:05 - 00:19:00)
Plot hole: When Blake teleports to XK72 to meet Professor Kane, he takes 2 teleport bracelets so that Kane can return to Liberator with him. When Avon goes over to retrieve the medical assistant, he neglects to take an extra bracelet. The assistant beams over with one anyway, and Avon somehow still has a bracelet to return with later. (00:34:05 - 00:41:30)
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.