I've encountered something that looked almost exactly like this before and it was caused by brake pads getting so low that they got to metal on metal which threw little rusty bits all over the place.
The vehicle in question was fitted with painted alloy wheels with a metallic silver finish and a lacquer clear topcoat. I tried all ways to remove the rust and the only thing that eventually worked was to take the wheel off, stick it up on the bench and manually cut it with cutting paste. Even then it took a good hours work to get the wheel back to immaculate condition. I have to say, although this worked, if I ever encountered this again or had a full set of wheels in this state, I'd consider refinishing them as it would probably take roughly the same effort.