My best guess would be that it is an issue with the wireless communication system in the game. AFAIK The game launches into local Wi-Fi mode when entering the underground, so you can see nearby players walk around and do stuff, as well as secret bases. I would guess that MelonDS does not quite know how to emulate local wireless connections as I too am struggling to get a local connection set up between me and a friend. However this guess may as well be useless as its perfectly possible to have a second instance of MelonDS running parallel to the original instance and to have the two find each other in places like the union room. I personally use this method to clone make backups of my favorite Pokémon on a second save file.
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