Visible crew/equipment: While Rygel watches over John's body, Rygel performs his own version of the Hynerian Ceremony of Passage to declare John dead so as to claim John's possessions, and when he pulls at John's boots, the puppeteer's arm/elbow becomes visible behind Rygel.
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.
Chosen answer: It's never explained. John mentions a theory that his less technologically developed craft simply interferes with the wormhole less than the "superior" Vipers, but they never make a concrete determination on that point. But we also have to take into account the fact that Moya traverses wormholes with no ill effect as well.
Garlonuss ★