I've only played this game on the new system, so I don't know if it happens on the regular 3DS with the Circle Pad Pro.
Anyways I've noticed that while playing the game, the camera seems to randomly freak out for a split second. As in the the image flickers to a random position every now and then. I couldn't exactly tell what was causing it, as nothing seems to fix it (I even turned off motion controls), but now...the C-Stick suddenly stopped working altogether. No camera movement, calibrating it via Majora's options menu does nothing. I had to save my game and exit the game (dunno if that was enough, but I turned off my system as well), thankfully the C-Stick wasn't actually broken and started working again when I opened the game.
That said, really hoping this gets Nintendo's attention, I go to other forums and it looks like I'm not the only one with this issue. Hoping they'll fix this in an update soon...