Whenever I leave an area with bees they despawn one by one until there are none left.
At first I assumed I just lost track of them, however, after creating a greenhouse to keep them in a small enclosed area I figured out they were just disappearing. When I first created my greenhouse I had about seven bees but about 10 in game days later there is only one left.
Haven't been able to reproduce this. Have you considered it a byproduct of MC-164594? Otherwise, this is a duplicate of MC-168008.