However, many of the errors have to do with via to polygon clearances and not differential pairs.
I see:
Clearance Constraint (Gap=0.085mm) ((IsRegion AND (OnLayer('L2') OR OnLayer('L11')))),(All) .................................................. ......... 864
Clearance Constraint (Gap=0.075mm) ((IsRegion AND (OnLayer('L2') OR OnLayer('L11')))),(IsVia AND (HoleSize <> 0.1)) .................. 0
Hmm .. I do not really know how this is possible. I do not have the old Altium installed to check it, but this is weird. When we send data to manufacturing, there must be no errors.
You can simply fix this problem by re-building all polygons (right click on the polygon -> Polygon Actions -> Repour All), but still, that will not answer the question how this is error could happen. Good point!