I don't know much about the glitches in the game but I can say that my copy constantly froze. It was random and usually only after I hadn't saved after awhile . If you haven't bought the game yet, I suggest the regular DS version. ;]
These are the things Natsume suggested: Stop doing the petting game Don't take your cart into the mountain Turn off the wifi and 3D Save daily Power off system every few days
What worked for me: 2nd 3DS lol
The reason this worked for me is that my daughter used mine all the time to watch Nintendo Video and browse the store. Seemed like as soon as I got her her own, I stopped freezing. Which leads me to believe that the memory leak Natsume claims causes the leak is tied to the system's use. Meaning, I think the game utilizes the systems memory and if you're using it for other things than you should power it down before you start your game.
I do exactly as Veggie, no petting mini-game. It's been almost 4 in-game years without a single freeze. I use wi-fi on and full 3D, if that matters. Ah, and my cart never left the farm, unless moving farms counts