It sounds to me like you are talking about a painter's phenomenon called "sandscratch swelling" or "die back". Do the scratches appear to be "in the paint" rather than "on the surface of the paint"? If so, this is what you're dealing with.
This condition is rarely seen in factory paint but can be quite common in run-of-the-mill production repairs.
If the color you are working on is solid, i.e., black, white, red, etc., without any metallic, then the scratching can usually be sanded smooth and polished to an acceptable finish. If the color has metallic in it you will never get rid of the appearance of the scratches. Even if you sand the clear coat to a smooth finish the scratches will show up in the metallic color beneath the clear.
The cause of this condition is the filling of scratches with primer/surfacer, when those scratches should have been removed before applying the primer/surfacer. The solvents in the subsequent topcoat(s) will "swell" the primer/surfacer and then as the finish dries/cures, shrinkage will occur and that combination of swelling and shrinking will result in scratches below and through the finish.
If you are working with a metallic color the only way to properly repair this condition is to strip the entire area, ideally to bare metal, but at least as far as the offending scratches in the previous repair, and redo the repair with proper sanding before applying any primer/surfacer or topcoats.
If the color is solid it maybe possible to sand out the scratches and then polish.
Probably not the news you were looking for - but unfortunately this is probably what you are dealing with.
