Yeah, you've got rust pits in the roof. Not uncommon. You can try using a wire wheel if the pits aren't too deep. Phosphoric acid (aka Ospho) available at your local hardware store will convert the rust to iron phosphate, but most epoxy primers (which is what you should use) aren't compatible with phosphate treated metal. Check with your primer supplier. Evaporust makes a gel product which is different than Ospho, and will remove the rust, however, I'm not sure of the compatibility with epoxy primers. Again, check with the paint supplier. The REAL way to get rid of rust in pits is to sandblast, then immediately prime after a grease and wax remover wipe-down.
