Maybe a purposeful feature, but Dispensers will Eject a honey bottle from a dispenser unless there is an empty spot available. This follows Water or Lava buckets, but Honey Bottles are a stackable item. So even if I have a slot that already holds honey bottles, the new honey bottle is ejected. 

I've attached screenshots of before harvesting and after. Clearly the bottle of honey should stack with the one in the dispenser slot.