I have the same problem on my Animal Crossing 3DS, only mine are thinner and there's about 5-10 scratches all along the hinge. I am not sure what causes it but I think maybe pressing too hard to close the top half presses the hinge down some to the point it scratches against the bottom half. I haven't been bothered to fix it because it'd probably just make it worse. I know it's annoying but just be thankful your 3DS is white so it's not that noticeable except under certain light conditions. If it was another color it'd be very noticeable. I mean you could go the route to spray paint over it with some matte white and just tape off the entire 3DS. Would be an easy project but you'd have to do extremely light coats.