Most of the bees are invisible ingame and missing from JEI. Issuing a /reload command seem to fix this, but only until a client is restarted. Singleplayer worlds are not affected. Tested multiple mod and forge version combinations, with or without optifine.

Before /reload

After /reload

That they are often missing in JEI is a known issue, but are they also invisible in game?

The bees are there in game, but are invisible and you can't interact with them. The combs are generated, the bees are working, you just can't see or do anything.