Additionally, you don't say how often you drive your auto. If it's a few days between uses, I've found that in wet weather conditions, it's truly amazing how fast small rust spots can occur on the brake discs or rotors as they are generally are called here. They're most often made of cast iron which rusts quite readily.
Here in the western U.S., it's fairly dry, but if we have rain or wet snow and don't use the car for 2 or 3 days, we'll experience what your describe but only for the first application of the brakes, since that, apparently, removes the existing rust…