The Bees are bugged. After some time playing in a server while having some Bees inside a Bee farm (or even Bees wandering around; not in a farm) once they get inside their nest they NEVER come out again.

Seriously I am not sure what is causing this issue or how to reproduce it but it's a thing and please take a look at it and fix it.

From my understanding, I think the nest is actually causing the bug. Maybe it gets somehow glitched and seems to be "losing" the Bees inside of it. I think maybe the weather or sleeping (which both affect the Bees' behavior) seems to play a role at this. Maybe a combination of them at a random, but exact, moment causing it, I don't know, (sorry for the lots of "maybe"s there but seriously I have no idea what is causing this bug to occur).

This bug first occured when I had a Bee farm in the Nether. I had 8 Nests of 3 Bees each. After some Days (Minectaft Days), idk, all Bees inside the farm where gone. I moved the nests in the overworld but Bees didnt came out. I broke all the nests and no Bees came out. So the Bees where glitched and disappeared.

Then I built a new farm, in the overworld this time, and after some days of working just fine the Bees again dont come out of the nest.

How to reproduce this glitch:

1. Start a Single Player server and build a Bee farm.
2. Play in the server as a normal player would do for some days.
3. The Bee farm sooner or later will stop working and the Bees will all disappear.

EDIT: I forgot to mention that the overworld farm that I built in my example even had nametag'd Bees.