Clean the die, Make sure you keep it clean as the lube left in it will pick up dust and crud, and uncleaned brass can deposit crud in the die as well. lube attracts crud and dust. That is what is causeing the scratches . Other than cosmetic they will not hurt much of any thing except that over time the crud stuck in the die will migrate back to loaded catridges and then can get into and scratch the inside of the chamber. So just make sure every thing is clean. Brass , Dies and finished ammo, it only takes a second to wipe things down.