You don't mention what type action or what manufacture your rifle is, nor how many rounds have been fired though the rifle.
If you open the action, drop a cartridge into the chamber by hand and close the action then eject the cartridge do you still have the scratch?
I agree, the bullet is probably rubbing as it comes out of the mag and into the chamber. It could also be rubbing when it gets extracted from the chamber and thrown out of the action. The scratch on the bullet, depending on how severe it is, probably won't affect the accuracy much if it's just a light scratch. You might need to have the action smoothed and tuned if you want to eliminate this or, it might work it's self out over time and several hundred cycles of the action during the course of firing the rifle.
More information would help.