I don't know if this only applies to existing levels, or if entirely new ones can be affected, but during LPV's conversion to new formats, I encountered this issue with the final level (which has 3 talismans).

It saved them such that there were two talismans with the ID number 2. The result of this was that one of them became impossible to unlock (and I suspect, meeting its conditions would have unlocked the other one instead, though I didn't test this finely).