Visible crew/equipment: Zhaan is talking to Tahleen as they've recently landed on the planet. When Tahleen says, "Perhaps our many cycles of reclusion contributed to an error in judgment," you can see the shadow from the camera moving on Zhaan.
Visible crew/equipment: After Tahleen alters John's memory of himself as a young boy playing in the water, and then Aeryn tells John that he's the most bizarre creature she's ever met, when it cuts back to Moya as Rygel joins D'Argo, you can see the head and movement of one of Rygel's puppeteers as D'Argo and Rygel are talking.
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 ★