When using dispensers filled with empty bottles to harvest honey, there is a strong likelihood of receiving honeycomb drops instead.

I have a farm with 12 beehives harvested by dispenser. All dispensers are filled with bottles, but I am still receiving honeycomb drops. For test purposes, I cleared out my output chest and watched the results for a couple of in-game days. In that time I harvested 19 honey bottle drops and 7 honeycomb drops (21 honeycomb). So, even with only bottles in the dispenser over 25% of my harvests were honeycomb!