Thanks for playing! Mushrooms actually never produce resources automatically - instead, they spread and upgrade, and you get mushroom resources by "harvesting" the units (i.e. by right-clicking them in the world). So I believe it's working as intended after restarting. It's meant to be similar to gathering mushrooms in real life.
And "adjacency" is 8-way! Sorry for not making that clear.
And storage is the amount of produce you can carry from one day to the next. So you can temporarily be overstocked if the current day's production pushes you over the limit, but when you click "Next Day" it'll discard any excess produce before doing the calculations for the next day. It's sort of like a hand-limit in a card game, if you're familiar with that kind of system.
I will add these clarifications to the game's itch.io page. Thanks for the feedback.