hi, in chapter1 in some missions, the mission description shows that you have the item if in some point after receiving the mission you have it in your bag, and it is not changed if you use it for something else. for each of these side missions, check if you really have all the needed items- maybe you already used the beer for example and need to buy another1.
automated harvesting lets you harvest everything from the farm house. this option is available after it's research if you do it befor harvesting anything the same day.
you should join the discord server to ask questions there, its faster :P