One of my past cats.
The game throwing up a error on the DSTwo is no surprise. It's able to emulate most gba games, although it has issues with modified ones.
I do know that newer VBA emulators have some issues when it comes to rom hacks - Specifically, the VBA-M line, but it shouldn't cause this kind of issue since you haven't modified any of the pokemon.
Are you using JPAN's hacked engine as a base, or a standard 1.0/1.1 rom?