Another possibility is paint on a finishing putty surface. Finishing putty will always have pinholes in it so that is why a high build primer is advised. If you sand through the primer you can have a result similar to yours so reapplying primer us highly recommended.
Another possibility is primer shrinkage. If the high build primer is applied and allowed to cure then sanded, it can shrink into the pin holes of filler and or finishing putty afterwards. The solution here us to leave primed panels unsanded for a week allowing all solvents to leave. Priming over filler with heavy scratches will also show up as a failure in the paint.
