If you stand and watch bees exiting their hives, they will occasionally get stuck partially in the hive upon exiting and then take suffocation damage until they die, or are pushed by another bee or a player. Notably, I have only noticed this occurring on hives where there is a block in front of the hive and and down one block. This occurs with a full block or a trapdoor if you are using trap doors around a campfire underneath the hive to prevent bees from killing themselves on the fire. The presence of another block in this location seems to interfere with bees exiting their hive and results in them exiting partly inside the hive block itself causing suffocation damage to occur. I have attached a screenshot of a bee dying in this manner. The second screenshot is of an automated honey farm in which bees will have the same bug. Its not as much an issue in the farm because the bees are usually nudged by others quickly enough.