I had the same issue and it scratched my CalSci shield as well. I emailed Madstad in November. Here is their response:
I don't know how the brackets scratched up your stock shield, the rubber bumpers should have kept the plastic off of the metal. Scratching happens when two things rub together, but when the shield is bolted down it should be immobile, so I'm not sure how they rubbed together to create the scratches. We've sold thousands of these brackets worldwide in the past 3.5 years and you are the first that has mentioned scratching.
One solution would be to move the bumpers outward a bit. You can carefully peel them off and re-stick them. If you want, send me your address and I'll send you an extra set of rubber bumpers so you can have on each side. If that doesn't keep the shield off of the metal then I don't know what will."