Did you, by chance, use a lot of filler on those parts and end up with air bubbles in the bondo? That will tend to make the primer do that, at least it did it to me when I painted a jeep. I ended up slathering on a very thin coat to fill the holes and re-sanding on top of the primer to get it to go away.
Don't use the glazing putty that comes in a tube, it is not good stuff to use under modern paint.
