Yeah it's the pressure being applied to it from the case, I have two cases, and it does the same thing. I put the manual inside to see if the added cushion would offset the pressure, sure enough it does, however.. it will lose it's place once in awhile and thus the system becomes unresponsive. This happens on both cases, the teal and the black versions. The cases were brought from gamestop and pdp.
Not sure why my 3DS is having issues with it, but it cannot be inserted in either cases without issues, unless again I put the manual and a folded napkin to offset the pressure. It's weird, not sure why I'm the
only one with that issue xD.