Till the Blood Runs Clear - S1-E11
Revealing mistake: While John and Aeryn are in the module, which is leaking plasma, just as Pilot tells them that Moya does not want to put her baby at risk, we can see the puppeteer rods controlling Pilot's arms as they move.
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 ★