I've seen this question pop once or twice while searching the forums, but nothing in the way of answers:
My 3DS seems to be having issues with sleep mode, among other things, seeminly only while playing DS games. I started playing Mario & Luigi: Bowser's Inside Story, and would regularly put the system in sleep mode whenever I had to step away from it. I noticed that on more than half the occasions, the system would soft reset to the home menu, losing any progress I had made before saving. Not only that, but several times, while the system was supposed to be sleeping, the speakers would make sounds and noises, which after paying attention, I figured out were actually random sounds from the game. It wasn't just playing the sound normally, it was a seeminly random assortment of bleeps, bloops, and electrical pops, but they were on closer examination, the game's soundtrack. I also noticed the game would freeze or crash whenever the system was moved slightlym which is a problem on a handheld held in my hands, and is an even bigger problem in a game that requires you to turn the system sideways for cerain sections.
At first, I thought it was just a bad cartridge, and just got through it, saving compulsively and keeping my hands steady. However, I started playing 999: Nine Persons, 9 Hours, 9 Doors today, and noticed that when I closed the system and put it to sleep, it also had soft reset to the home menu. I've had the Zelda 3DS XL bundle since launch, and never had any problems until recently. I went maybe a month without playing anything on the system, and started playing it again for M&L:BIS and that's when I noticed the issues. I'm going to try to recreate the issue with various other DS and 3DS games, but I figured two games in a row crashing are worth going to the tech support forums.