Road Debris can include small bits of iron, they get flung up onto the paint and create a rust spot. The good thing is that they rust on top of the clear coat instead of underneath it. So you may be able to scrape the iron filing off with a fingernail and clean the rust off (Meguires ScratchX works really good for that).
If it's throught the paint an the metal underneath is rusting then you have a bigger problem. You can try rust-stopper/sealant and paint over it but rust is like cancer. It has a tendancy to work its way under the paint, so you may have to sand off the rust and repaint the sanded area.