It would be hard to scratch a barrel like you describe unless you were try to remove an obstruction with a steel rod. I think chances are good that's just a smear of lead rather than a scratch. Try the "chore boy" method (you can search it out on this forum) and I'll bet your scratch goes away.
As to the "why", could just be a rough spot in the bore. I usually give all my new-to-me guns a good cleaning with some of the felt pellets from Brownells and some Butch's Boreshine, followed by Borebright. A little polishing is not a bad thing in a barrel.
Link to the cleaning pellets:
WEAPONS CARE SYSTEM PELLETS | Brownells