Wilds are causing me a problem too. For now I'm just hoping the next build will fix it, but if @Kaphotics doesn't know what the problem is, I'm not sure that'll happen.
Edit: Actually, I'm stupid. Even closing the Wild Encounters menu without changing anything makes pk3DS crash, which seems like a super important piece of information. It's not the randomizing at all.
Edit2: Finally found a download for the Dec 10th version mentioned last page, which isn't giving me this issue. https://mega.nz/#!Eo8WUbzZ!SDnRu1dvLr-p2YTBc1csEuNj9yscT061iSpzX4LXYB0