When I use /kill @e while there is a bee in a hive/nest, the bee stays in the it. When I break it later, the bee comes out despite the fact that I have used /kill @e.
TO RECREATE:
Spawn a bee next to a bee hive/nest and flowers
Wait until the bee goes into the hive/nest
Use /kill @e
Break the hive/nest in survival
Pretty sure this is working as intended, as bees are no longer entities when they are inside a bee hive/nest. Instead, their NBT data is stored inside the hive's
BeesNBT tag.