The Pokémon Mystery Dungeon Adventure Squad series, like all other Pokémon games, have Pokémon in each version that are unobtainable in the others. In the main series, you would trade these Pokémon and in the Mystery Dungeon games, you typically get them by linking up with the other games. The Adventure Squad series is no different. As there are three games, each with their own theme, the Pokémon are spread more evenly across all three games. As you can link game saves across all three versions, it should be simple to get a full collection.
There are 92 Pokémon that are obtainable within all three games, but the vast majority of the Pokémon are only available within certain games. This page and the respective pages are to detail what version each Pokémon is exclusive to so if you're only getting one, you can make the right decision. As the Pokémon number in the hundreds between versions, they're on their own pages.