It appears that Bee path-finding doesn't cooperate with low Y coordinates. On a private vanilla server, I have a base that contains an underground village roughly at Y=30. The bees inside of the village repeatedly keep trying to wander upwards for seemingly no reason, often getting stuck on the ceiling (which is roughly 15 blocks tall). The only solution I've found for this so far is holding a flower near them to get them to come back down.

This has also been noticeably a problem at an industrial complex centered around a guardian temple on the server, which has seen bees escape up and out across the ocean. I started with dozens of bees at the complex initially, but I found only two left after only a couple of real-life days (the area is almost constantly loaded over those couple days).

I have seen a couple other issues posted on here relating to bee path-finding issues, and I feel like this may be the same issue but manifested differently.