Guys, for everyone that has that issue. I've got it after going back to main menu, i think it was right after casino.
And for me what fixed it was Alt+Enter(twice).
You can use this setup. Furnace has 2 wrenches inside of it. Bread conveyor is at speed 2. All logic gates are connected to one spot. And the logic gate at butter is reversed.
Basically what it does is putting butter until its full and when recipe is done it stops butter from going for a brief second so that other materails can go to their spot. Same can be done with fossils fuel. Just make sure to put gates very close to funnels. Other than that it is kinda simple. (in my first playthrough i also thought about automating it and spent like 2 hours experimenting)
I think, it would be better if you changed a hovering hand's description so it mentions that it can grab items from storage/machine. (that could have saved me some time)
Also i noticed that clicking on Soft Cheese item in recipe book shows that it is an ingredient for hamburger, but it is actually not.