Thanks for the report, and the detailed example.
This is kind of a strange transition list. It concerns a single molecule "Mol1" with two different kinds of ionization, which is fine, but it's unclear what those are. Whatever the two adducts are, they result in an ion mass difference of more than 200 AMU, which is remarkable.
My guess is that these aren't really different adducts of the same molecule "Mol1". But, since the transition list says they are, Skyline tries to puzzle that out using the mz and charge values it's been given. Clearly Skyline is getting this wrong, but I'm not quite sure how to get it right. Can you describe the intent here?
Thanks for using the Skyline support board!
Brian Pratt