The salt bath nitrading process S&W uses is significantly harder than Kydex. You do not likely have a scratch but as mentioned above some Kydex residue. Easy to get off.

You have already probably prevented it by removing some material from inside the holster, but don't assume it is at the bottom of the holster. It could be higher up. The gun will wear in the holster. Keep cleaning the residue off the gun until it stops depositing. You'll be fine.