If you set a hidden item that can only be gathered once in the item priority window of the gather manager you will end up collecting that item, however when the item is no longer available (limited collections) it will keep clicking the spot that now says "Nothing" and stop gathering all together.
Bumping this since it's still an issue.
Are you using beta or live bot ? what item are you trying to gather ?
You can't set gardening/maps to a slot in gather manager. The client still sees the item, even after it's been gathered, so the bot just thinks it's still sitting there. This is why it's an automatic process in beta (and soon, somewhat optional as well).