The steel wheels on the base are just painted black and you put a hubcap on them, right? I'd think it is doubtful that you'd be able to claim this under a warranty, but it can't hurt to try.
FWIW, my other car is a 12 yr old Subaru Outback Sport. The steel rims on it have been showing a little light surface rust like you describe for about 4 or 5 years. I did fix it on one side, but never got around to the other side.
Assuming it isn't covered, I would suggest that you just try cleaning all the brake dust off the wheels, then hit them with a wire brush (I like the ones you just attach to a drill) and thoroughly cleanup the rust spots while roughing up the black finish everywhere else. Once you've done this, you should be able to prime and/or repaint the wheel using the paint of your choice. (Presumably, you'd want to use a flat black spray paint.)
2007 Flint Micah Rav4 Sport 4x4, i4
1999 Land Rover Discovery II
2006 Subaru Legacy GT Ltd (Sold) :-(
1998 Subaru Outback Sport