Does the Pokémon Bank know I got the first evolutions of a non-alolan Pokémon

Did you talk to Brigette explaining whether you wanted 100 pokemiles or 10 battle points? There is also a 3rd option, to not receive either, which you may have pressed. I believe re-entering the pokebank application will bring up a conversation with Brigette where you can choose.

According to Serebii, you will hatch a Alolan form of whatever Pokémon you are breeding, by default, if there is one.

When you transfer Pokémon from previous games and breed them, you will get their Alola Forms. However, if you attach an Everstone to the non-Gen VII native variant and breed, you'll get the standard form.

Thus, if you breed two standard Dugtrio, you will get an Alolan Diglett. The only way to not breed an Alolan form is to have the standard form parent hold an Everstone.

As mentioned in the comments, this means that breeding a standard form Pokémon with a Ditto holding an Everstone will still result in an Alolan form baby. In order to get a standard form baby with one of the parents being a Ditto is for the non-Ditto parent to hold the Everstone.