When Kryten takes the syringe out of Lister's head, the needle does not come out the syringe properly, so Robert Llewellyn puts his hand in front of the needle to try hide it.
When Rimmer first inhabits Lister's body he remarks that he can smell, as if he has been unable to as a hologram. But there are several times he has mentioned smelling things as a hologram, such as when he could smell camphor wood of his chest burning that he thought was Lister's guitar.
When Lister and Rimmer are in each other's bodies, their mouths are frequently out of sync with their voices.
When Lister's body is taken over by Brown (a woman) and later Rimmer, he wouldn't sound exactly like them because his vocal chords would be different to theirs. Although since Rimmer is a computer generated hologram, it is feasible his voice could be changed to sound like Lister's (who as an official Red Dwarf crew member could also be generated as a hologram)
The shadow of a boom microphone can be seen when Rimmer (in Lister's body) pretends to have lost an arm.
Lister refers to Blue Midget as "White Midget" when trying to persuade the Cat to let him borrow his body so he can fly it.