If those are not material transfer and bona fide reduction of paint down to primer like they seem to be, an approach I used to amazing effectiveness recently is to:
1) Clean area
2) use a sponge or bit of microfiber cloth to paint over the area with dealer-supplied matching color paint (the stuff that's $7 in a little vial--just paint the sponge or cloth first, then rub it over the entire area of the scratch
3) Give it a very short period of time to dry (dries almost immediately in just a few seconds)
4) Buff area out with Scratch X 2.0
End result is the scratch will still be there and its damage will still be noticeable when clean and at the right angle of light (even though its trough is now matching paint color) but it will look tons better and is likely to get it to where you need it to be. Using touch up paint is very hard to get a clean, nice application of it by itself. That's why the sponge approach so that it's on thin followed by Scratch X. After the paint is applied the scratch will be filled (good), but also you'll have painted around the scratch area (bad), so a quick go with scratch x solves it. I've done this on two cars this year to satisfying effect. It's not perfect, but neither is the rest of your paint. To get a showroom shine will take a great deal more effort and skill and time than I've mentioned above.
My approach works ideally with thin scratches, so that the scratch x kind of jumps the gap. I imagine it would need some revision for wide area patches that have to be done. The approach above is pretty safe, though and doesn't take much practice. I kind of borrowed the idea from some detailing sight in which a guy used a similar approach but wet sanded it down after applying the touch up paint.
