The cause is different behavior on trying to load invalid sprites; to my understanding, the NDS keeps reading until the address wraps around to a valid sprite, locking up until then; other hardware stops reading immediately. That scenario has a problem with one particular animation when the map reloads after a battle. It seems plausible that other games would have the same issue, but MMBN4 Blue Moon is the only one for which Nintendo's got an acknowledgement of the issue on their site, so maybe literally nobody else made that mistake.
I wonder whether they caught that? On the one hand, it's a (relatively) known issue, in that Nintendo has mentioned it on an official support page. On the other hand, it seems to only impact a single scenario in a single game, which has a load of other bugs anyway. But then, they're not trying to support DS games, so the only way for the bug to get in (if they're going for an as-close-as-possible emulation of the GBA and doing so successfully) would be if the bug does in fact cause hangs on the SP and they used that one as their reference.
[1] https://www.nintendo.com/consumer/systems/gameboy/trouble_sp... [2] https://lparchive.org/Mega-Man-Battle-Network-4-6/Update%200...