Into the Pit

Is there a way to check which ones (mixtures) have been already completed?

Yes diego you need to press X to see your tab for everything press RB two times to go to the progress and here you can see the dungeon you cleared and the mix you can do👍

Welp, Hiró. Looks like I never even thought to use that menu, lol.
I only checked all the shopkeepers and completely forgot about the "X" button menu.
I luckily remembered that I exited out of the village through the Xbox menu and not the in-game menu. Then spawned at the Fungal boss, instead of at the village. So I just narrowed it down like that, redid three dungeons. Turns out it was the third dungeon from the start of my game.
I just did all 15 dungeons, one key purchase at a time. Doing every possible combination before buying another key. So I didn't get confused. But the glitch messed me up.
Maybe the menu would've been bugged anyway, if I checked. Cause the game still let me have all 45 villagers, before the 15 dungeons completion

Welp. Somehow crapped up for me, with the achievement at 93%, even though I popped the 45 villagers achievement.
I think I exited the game improperly at one point and one of my dungeon completions didn't count. I vaguely remember a time where I spawned back at the boss of a dungeon. Even though I exited the game after getting back to the village.
Now I've gotta go through all the dungeons all over again. Hoping that I don't regret doing it on the same save, if it still doesn't pop

Just want to note, if you make it to the boss of a dungeon, rather than do a whole run again to get there, use the same method as the Note farming and close the game when it says 'Press A to continue' after dying. Load the game back up and you'll be back at the boss fight prior to dying.

Credit to I ima Pokemon I for letting me know this!