Spots on paint don’t go out

Hello Together With my Mercedes GLA 200 I have many small stains on the roof (see picture in the appendix). At first I thought that they are paint damage (stone strokes), because they are small white dots. If I drive over them with my hand, the paint is rough. In the workshop they said that it might come from a tree (but no longer know which one). With the fingernail you can remove them. How to remove them best (with the fingernail is a bit elaborate) ? I’m not in the wash road and after the workshop they were still there (there the car was also washed). I used the Sonax MultiSwmm 2 in 1: https://www.sonax.de/…/multischwamm-1-stück I used only the gray side and so it didn’t go out. Could I also use the white side or can make this more scratching in the paint?