There is the one everyone is aware of, when you go to enter the restaurant and meet Honoko.. but be aware, just HAVING that mission will lock you out of one of the NPC’s romance storylines too, where you’re supposed to meet them in the very same restaurant.
Because the two conflict, you’ll be locked out of finishing that romance plotline.
Finish the companion quests before you go too deep into the main storyline.
I was hit with this particularly annoying issue. Ces’t la vie.