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 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)
