Good idea Athiril, I just tried, using a razer blade. It looks as if some"flakes" are ON the surface and possible to cut/scraping away (typical on the non-emulsion side!) and some not. The explanation should reasonable be that some "flakes" are "hole" in the emulsion, and some of these emulsion pieces are to be found on the film surface. Sounds reasonable to me, at least.
(BTW, a frame/sheet with this damage to the emulsion in not totally ruined, at least with scanning and with a quite easy retouching nothing looks wrong; though perhaps not optimal for a regular print.)

Thank you Athiril for your interest in the issue and very good suggestions (have never experienced this kind of emulsions problems, but your choice of the word "flake" rather than my "spot" really pointed to what seems to be a reasonable solution!)