I haven't heard of that happening, but you may just want to directly contact Nintendo support, so that hopefully some sort of bug report gets started in their system, and either some kind of New 3DS firmware update can fix it, or (maybe less likely) Nintendo gets AlphaDream to patch the game to a version 1.2 that fixes that issue.
If I had to wildly speculate, some visual effect related to the purple monster exploding does not deal with different CPU very well.
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