Doesn't happen a lot, but on more than on occasion I'd be holding a long hold note and it would just drop. and once in a whole I'll hit the screen for a normal note and it would fly on by into a miss like I hadn't hit the screen at all.
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The one I get more commonly, but still pretty rare, is the cursor getting "stuck" in FMS when near the top. When I try to move it back down, it won't, and as a result, it drops the note since I missed a trigger. Cursor will reset for the next note, but when it happens, it is not uncommon for it to keep happening throughout the song if the cursor needs to be moved up high again. Not sure if this one is the game itself glitching, or simply my 3DS screen not being sensitive enough in a certain spot near the top of my screen.