The Mystery Zone caught location isn't shown in Sun and Moon (or gen 6) which suggests it's removed from the Pokémon's data which would also explain why it isn't rejected for being problematic.
In Diamond, Pearl, Platinum, HeartGold, and SoulSilver, there are two "Mystery Zone" headers: 0000
is for maps while 07DC
is a caught location. All games afterwards have a single "Mystery Zone" header that goes unused.