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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.
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 ★