Basically the title, I can't control click items into a brewing stand, instead it just moves it from the inventory to the hotbar or from hotbar into the inventory.

26b7183 fixes one part of this, but the shortcuts only directly support automatically targeting to chests -- the same thing will happen on a furnace or crafting table, etc.

You can use the ctrl+up/down shortcuts to move to the section 'above/below' where the item currently is however.