The paint pulled off with a thin coat of bondo in these spots showing the white primer coat below. So, I'm not so sure auto bondo is the best thing to use other than in areas of deep fill. I'm going to have the painter come back and try to fix things. If you absolutely must use body filler to make the repair, then you should remove all the scale, add a backup screen to cover the holes from the back side, then use Bondo Bondo-Glass over the rusted area, sand and finish out with regular Bondo body filler for a stronger repair. Mix. The mix is crucial.
Use Bondo® Glazes for contouring and finishing surfaces or repairing minor surface imperfections before you paint. Each product is self-leveling and easy to apply and sand. Bondo® Hardeners are designed to work with the Bondo® Fillers during the mixing process.