Your statement that it looks like its happening in area's with body filler may be correct.
This was a major problem when basecoat/clearcoat first came out
light colors such as white, pastels, some silvers after the paint dries would Bleed or stain the paint. This sometimes would take
30 minutes to show up and sometimes 2-3 months later.
This problem was blamed on putting to much hardener (peroxide) in the filler and yes that could help cause it but was not the real cause. The bodyfiller companies made major resin changes back then to help stop the problem and the clear manufacturers also had to do some major revisions.
It rare to see this happen today but it sure can! When you see the problem pop up today, its not the filler usually doing it, its a two part glazing putty.
To cause this problem there MUST be abuse to get the yellowing results and heres how.
Rushing the product.- Sanding the filler right away and than applying primer. You see this a lot with dealerships doing warranty type work (small dings)
Full repaints- The fillers are not going to bleed because of how large the job is as they have enough time to dry but last minute before painting the painter hits all the bad spots with a glaze and sands and right away applies sealer and next day little yellow spots.
To repair-
*Sand and a coat of epoxy is about a 95% (not 100%!) corrective repair. The stain can bleed back through the epoxy.
*2K primer is about a 30% repair chance in your favor.
*2K sealer is same as 2K primer.
* Waterborne primer is a 100% sure cure.
Ideal way to repair is sand clear off in the problem spot and set it sun for a few days or use a Short wave lamp to draw rest of stain out than epoxy and repaint..
Bottom line what causes staining is applying the primer to soon.
