Additionally you want to make sure to talk to the professor again when going through the walkthrough to church check up on all locations. Once you complete the quests, the parrot stops hinting at him.
From the PC users who can check & edit their save file, most missed the walnuts from the singing stone cave after falling asleep while receiving them.
For console users, I guess the only solution is to recheck all locations with a good walkthrough, and if confirmed they are not missing one, wait for a patch to fix the problem.