In Sun/Moon, make sure your PKMN don't stay in Isle Avue
I noticed that, during my initial transfer from Bank to Home, some of my favorite Pokémon didn't make it over. I found them lounging in Isle Avue. Don't leave them behind; transfer them from PokéPelago back into a box.
Similarly, and I'm sure this is already well known but it bears repeating: if any of your Pokémon are registered in a battle team, you must unregister them in order to transfer them to the Bank.