The frame of the lower screen, the raised part, seems to touch, the upper screen when closed, or when some pressure is placed on the outside of the 3DS, resulting in it leaving marks on the upper screen, which over time, develop into not so much scratches, but stains, akin to something grating the screen.
My original one did it, my replacement I put foam feet that my surround speakers came with.
Since removed them as a tip I got seems to show mine isn't affected.
The foam that comes with the 3DS in between the screens, place in inbetween the screens, and close the 3DS, press on the top lid(with the dual cameras), and open the 3DS, if there are marks on it, with the foam in, it won't mark when they aren't in...weird, but it seems to work..both mine and my son's replacements mark with the foam, but don't mark without it, when pressure is placed on the lid.
Both our first ones did it, and his was really bad, so much so, the top screen had 2 vertical scratchmarks on it, ON the screen, which resulted in a sort of sparkle effect when playing, but give them their due, Nintendo replaced both of them, without too much of a fuss for 2 split new boxed ones.
His replacement, a metallic blue one, and mine, the black one, both seem free of this strange phenomenon.
But I do notice now, that when looking at the top screen, with it barely open, it seems sort of bevelled, away from the bottom screen.