My worry would be the new site was put in wrong and damaged. As for the marks, that's not right. Any gunsmith worth his salt must have encountered this problem in the past. I have put in some different sites and it was not that I am a gunsmith. Maybe just lucky. I always masking taped the edge of the site, and the area around the barrel. If the dove tail is tight, like Sabotloader said, one maybe two strokes of the file is all it took to make that slide into place.

I think I would take the rifle back and show it to him and tell him if there are troubles with it, that something will have to be done. I am sure he is aware of the mess he made and that is why he decided he did not want to charge you for the mistake.