Continuity mistake: At the end of "Bad Timing", the final shot of the boat with Aeryn & John crystalized shows that their pulse pistols are still there and intact. But when they are reconstituted at the beginning of "The Peacekeeper Wars", the pistols reappear on their belts for them to draw.
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: When Aeryn fires D'Argo's Qualta blade at Plonek, it hits the Scarran multiple times on his left side creating a large bloody wound on his chest, and then John shoves the icicle into the right side of Plonek's chest. However, after Plonek pushes John to the ground, in the close-up the icicle is on Plonek's left side with no wound on his right, but when Plonek collapses the icicle is back on his right, and still the bloody wound is gone.
Continuity mistake: After Aeryn uses up D'Argo's Qualta blade on the Scarran who's after John and D'Argo, John grabs a huge icicle and plunges it into Plonek's chest with his right hand, but in the close-up John's using his left hand, then in the next shot the icicle's back in his right hand.
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.
Continuity mistake: After Oo-Nii tells John that the old woman stole his gun to kill Vella, John looks down at his holster and finds Winona gone. Later while he's shouting for Granny, it keeps cutting to the old woman while she's holding Winona, and after she whispers, "Receive the spirit," it cuts to John and Winona can be seen in the holster on John's leg, but in the next shot Granny still has it.
Continuity mistake: When John's at Serenity Base, in the shots from inside the pod when Aeryn looks out the window John's standing beside the flag and their long shadows are cast behind them as he looks toward Earth, but when John's on the phone with Jack, in the overhead shots the shadows are being cast in front of him.