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When Rol mentioned this, I googled it since someone had also mentioned this on a youtube video. I found a couple of stories on this but nothing concrete. I wipe my 3DS with Windex Glass Cleaner. I've seen these "scratches" on my 3DS above the analog nub and the touch screen but for me, they wipe right off.

I say give Nintendo a call. I'm sure you won't be the first and I'm almost positive that they'll repair the system for free (a guy in the comments section of a youtube video said this, too. I believe him because I'm gullible.). Some suggestions were to keep a cloth between the top screen and the bottom screen. I say just keep it clean (which you have been doing) especially along the edges of that bottom screen.