See this link:
Please add this to the list of bugs with Nest of bees, such as:
- Nest of Bees do not benefit from Chemistry tech despite being a gunpower unit
- Nest of Bees miss most of their attack and deal less damage than Mangonels as a result
Link for these two issues:
Haha, I ran into the same bug today. I had Nest of Bees in shallow water and would not damage a group of longbows.