I think DMT has a pretty good rep for making these things right, if you're worried about it. Might give 'em a call, see what they can do for you. Or, get in touch with the dealer where you bought it.
It'd be tough for me to say if it's a significant issue, without seeing it myself. But, the 'scratch' you see on the hone might just be a remnant of something that's rubbed against it. Being diamond, it'll remove material from anything that touches it. Might be a 'track' of whatever that material was, as opposed to an actual scratch. Sometimes that stuff will get embedded hard enough that it's difficult to remove by ordinary cleaning methods.