Confirmed this bug exists on 1.16-rc1, java 1.8.0_51
Added a screenshot showing the nest placement. One difference between the current and original (problematic) state is that I added the peonies and dirt next to all of the nest locations.
I realize that you're applying a policy that may have been decided upon by others; however, as a counterpoint to the policy-makers, this kind of response makes it unlikely that I'll be back to contribute more of my free time to making the product better.
Confirmed in 1.16 20w20b. A phantom was able to attack me through a wall of glass panes.
Update: I went out on another (in-game) night and harvested three more bee nests. This time some bees did remain in the nests, and one of the nests apparently had 3 bees, because I got the total bee-location achievement. When I placed the nests in my apiary, some bees did re-emerge. Bees emerged in my apiary both before and after I used the glass bottle dispenser to harvest the honey (which came back with the new nests).
I did change the apiary slightly prior to placing the new nests, to ensure that there were dirt and flowers within 2 blocks of each nest location (which was not the case on the first round of nest placements).
So, what is different that may have caused bees to relocate the second time but not the first?
It was not raining when I harvested the nests
Different iron silk touch axe that had no Efficiency enchantment (only Unb 3, ST)
Apiary flowers were planted next to the new bee nest locations
I did not same the game nor place the bee nests in chests prior to placing them in the apiary
I think we can rule out these possible causes:
Mod loader
Placement on / use of dispensers (unless the loss of bees is gradual)
Unknown game environment issue
So, I'm happy to have bees now, but I still think there may be a defect to be found.
I've had the same problem with huge patrols spawning on top of the roof of my house made out of unspawnable blocks in 1.14, and I think I might be also catching illager patrols spawning in light levels they shouldn't as well. Please fix this issue, my base is constantly being overwhelmed with illager patrols because of this issue.
This is still an issue in 1.18_experimental-snapshot-2. I've lost about 12-15 bees to water damage, with the hives/nests located on small islands in a warm ocean biome.