Continuity mistake: At the end, when Aeryn and John are with Little D, his arms keep changing from being swaddled to being free.
Continuity mistake: When D'Argo, who is followed by a few Eidelons, is walking to meet Moya's pod (with Chiana aboard), there are short shadows directly beneath D'Argo in shots facing him, but in the shot facing the pod there's a long shadow being cast in front of him.
Continuity mistake: When Crichton talks to Harvey (Scorpius in his head) about the Wormhole Weapon engineering project, one of the women in the scene leans on the hood of the car, with her glasses in her hand, chewing on the left arm of the glasses (the right arm is folded). The camera angle changes, and the arms are switched. The camera angle changes back, and the arms are switched back. (01:43:50)