I created a bee/honey farm in the overworld, consisting of about 48 hives (blocked by solid blocks on all sides, except the front-side) and was working on breeding bees to populate all the hives. After some time (several MC days) the bees stopped exiting their hives. A couple will still come out, but the majority do not. I copied the world and tried breaking the hives with a pickaxe (no silk touch) and sure enough there are bees in the hives and when the hive is broken the bees are angry, but they seem to no longer want to exit their hive.