I’ve noticed this a while ago, the farm resetting timer for itself when you collect it. In example lets say refill time is 2 mins. If you collect at 1:30 the farm countdown resets at 0 and 1:30 wait time is lost.
The way i tested this was not collect one of my farms(same level) and collect regularly as often I can with a small delay between bread was filled. The non collected one had extra bread then collected regularly.