Yeah, for a while I was afraid it was just me. Luckily, here is one of the forums I searched when trying to find what happened, so it's nice to know I wasn't alone:
http://techforums.nintendo.com/message/151628Anyway, since restarting I have played exclusively on my NEW 3ds XL and am pretty far in the game and no problems (so it is likely not the cart itself). I also haven't seen anything posted on this in a few weeks, so hopefully it is all fixed. If i finish the game soon I will test it out.
An like I said, I have no idea if that was the actual cause, but it is the only thing I can think of since I had barely played the game more than a few hours.