I haven't gotten any screen scratching. Then again, i'm one of the smart people to put a screen protector on. My silicone case wraps around buttons, and it does leave marks on the 3DS matte-textured plastic.
I'm pretty certain that it happens as a result of people putting them in their pockets when wearing clothes that aren't loose. If you don't do that, it probably will never be an issue (at least on the XL).
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Clean your screen often and clean the bottom part where it seems to be touching regularly. I usually clean the top screen with a nintendo cleaning cloth and wipe the frame of the bottom screen with my fingers.
Im thinking the screens are so close when the system is closed, that even tiny dust particles on the bottom screen frame will cause contact between the surfaces.
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