Continuity mistake: When Lishala gives John the map of the sky she asks him where his home world is, and John picks up a very small stone, but in the closeup he's holding a much larger stone in his hand, then in the wide shot it's small again before he throws it.
Continuity mistake: When Rorf and Rorg are firing at John and D'Argo who are pinned down in an area with no "back door," the lens surface on John's goggles are scratched/cracked, but once John makes the comment about soldiers of fortune and Aeryn walks out, the small holes on both lenses are now perfectly intact.
Continuity mistake: In the scene where Crichton and Crais are fighting with the chains in the room with the metal whirly-gig you see Crichton fall and Crais wraps the chain around Crichton's boot. In the very next shot you see Crais yank on the chain with all his might, but the chain is now attached to Crichton's hand instead of his boot.
Continuity mistake: When D'Argo, Aeryn and John start their search for clorium, D'Argo is wearing arm bracers which extend over the palm and back of his hands. After John says, "Pilot said you press this, this and...this. Works just like a VCR, except easier," D'Argo grabs the particle analyzer from John, but in the closeup of the particle analyzer the hands we see are bare, which means it's not D'Argo, then in the next shot D'Argo is still holding the device.