The question is what products are you using? Scratching swelling in body work can be caused by:
-cheap primer that shrinks too much and not applying enough primer film build
You should be putting 3-5 coats of a quality urethane or acrylic primer. Also most people do not realize that the final scratch in body work should be softened up before priming. 180 or some people do 220. I DA all hard block scratches that are on the edge of the body work with 180 then 320 feather-edge. You can prime over some hard scratches with a good primer and possibly get away with it. I have seen body work scratch swell months later by doing this though, especially with cheap primer.