Unless the spots are corrosion that is raised on the brass, load and shoot them. Just a colored spot in the side of the brass won't affect shooting.

Like others have said, don't tumble cases with unfired primers.

Lee makes a case holder that you chuck into a drill and you can spin the cases onto steel wool. That would remove corrosion or dis-coloration.

Brass cleaners like Brasso are not recommended for cleaning cases.

The primary reason to clean cases is to remove anything that would scratch your reloading dies or the chamber of your gun. Dis-colored cases shoot just as well as shiny ones do.