This was a recent support request:
https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=a175b41b-b099-1032-966e-da202582cf3e

And also an exception from Jan 20, 2015:
https://skyline.gs.washington.edu/labkey/announcements/home/issues/exceptions/thread.view?entityId=a4a1a307-82cf-1032-81a1-da202582d7c2

Exception type: AssumptionException
Error message: null object

Stack trace:
   at pwiz.Skyline.Util.Assume.IsNotNull(Object o, String parameterName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1580
   at pwiz.Skyline.Model.Results.Scoring.PeakFeatureEnumerator.SummaryPeptidePeakData.GetMzFilters(PeakScoringContext context) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\Scoring\PeakFeatureEnumerator.cs:line 402

Steps to reproduce:
1. Open attached file (Gasac_JL0005-Gill_GLIPR.sky.zip):
2. Edit > Refine > Reintegrate...
3. In the peak scoring model choose "<Add...>"

Result:
AssumptionException

This is an old one. Still a problem?

This assert no longer exists, and no similar bugs have ever been reported.