I experience this occasionally too, but only when I place the 3DS directly on top of my laptop's keyboard, and then it returns to normal once I remove it. I'm inclined to agree with @PhailRaptor of it being a hardware issue, probably occurring when something external causes the system to malfunction. I'm no hardware expert, but, in my case with my keyboard, some magnetic chip of the 3DS could have been reacting to a magnet within my laptop, or something of that nature.
Did you notice anything in common between the two times your game paused, in terms of where your system was, or something like that?
PS, I've had this happen to me about 5 times (because I love multitasking, and I forget not to place my 3DS on my laptop), and I've experienced absolutely no negative effects or corruptions to my game, so I don't think it's that big of an issue if it accidentally happens to you again.