Inspired by this support request:
When Skyline calculates the light to heavy peak area ratio for small molecules, Skyline tries to create a correspondence between the transitions in the light precursor and the transitions in the heavy precursor.
Part of the reason that Skyline does this is to be able to calculate the "ratio dot product".
The other part of the reason is so that if a user removes a peak from a light chromatogram (because of, perhaps, interference), the corresponding peak in the heavy chromatogram does not get added to the total.
This behavior is not what users expect for small molecules. Skyline's heuristic for matching transitions between light and heavy is not robust unless the small molecule transitions have been given names.
The most likely fix that we will do is to make it so this matching of light and heavy transitions if any of the transitions do not have a Name.