Your brass keys should only be about 3.0, and gorilla glass a 9.0- you should be able to rub keys into brass dust all day long and not mark the screen.
I store my keys right in my pocket with my glass iPhone SE, and it doesn't have a mark on it.
I suppose it is possible you have keys with some weird material or coating, or as another poster suggested- maybe something like an abrasive dust got stuck on your key.