Plot hole: Cat wasn't manufactured by the Jupiter Mining Corporation and had no connection with them, being born three million years or so after they lost control of Red Dwarf. The takeover by M-Corp would mean nothing to him. Why, then, does he become invisible to Lister?
Plot hole: In order to build up suspense, Virgil and Brains stand on the Crab Logger as its dangerous fuel is pumped out, despite the fact that it is hanging on the edge of a precipice. In fact they could have left as soon as they had plumbed in the pipes to empty the fuel tanks - the whole procedure is controlled by Scott in Thunderbird 1 and they make absolutely no contribution to the operation at all. They do not need to disconnect the pipes; they are left behind and dropped from Thunderbird 1 as planned. They just stand there chatting about how much danger they are in until jumping clear at the very last second. Silly buggers.
Continuity mistake: In the scene where William Fichtner is shown first leaving his trailer and picking up litter in the amusement park, his gloved hand switches from his right hand to his left then back to his right again before he starts talking to the couple. (00:05:40)
Visible crew/equipment: After Rygel's transport pod returns to Moya, as the docking bay door slides open, in the shot facing everyone while they have their weapons drawn we can see the bare floor. However, when Aeryn checks Crais for hidden weapons and then as D'Argo approaches him, there's a blue crash mat on the floor. Then it vanishes again.
Other mistake: Right at the start, as they're crashing, the computer narrates their rapidly-dropping altitude in feet. But the "altitude" dial we're shown is in metres. Most noticeable as they cross the 3,000 mark, when the computer voice and the height say/show the same number at the same time, despite the different units. 3,000m would be more like 9,000 feet, or 3,000 feet would be more like 1,000m. (00:03:20)
Continuity mistake: When Shepherd Book tells everyone about the electrical nets, Jayne says, "One day you're gonna tell us all how a preacher knows so damn much about crime." Shepherd then turns to leave. But in the immediate close up of him and Mal, he turns to leave again.
Visible crew/equipment: When Mulder and Scully enter the abandoned mine through a doorway, the viewer can see at right in the distance a number of people sitting on a wall, and one crouching in front of the wall with what looks like a dog. They are sitting still, but there is still movement there. (00:16:00)