When a bee nest/hive contains a bee(s) it earns nbt, due to it containing random UUIDS, motions and positions, you are not able to get a stack with multiple cuantities other than 1,

This affects the reading that a comparator does in containers with the item,.

For example a bee hive with bees, will output a signal of 1 in a hopper, but since it wont stack to other bee nests it should output a redstone strength of 3.

(Note that I am not saying that a comparators makes a direct read of the nest, but from a hopper with a nest inside)

On a side note, since no other item in game has the ability to make a transition from an item stackable to a non stackable, I would leave to developers to decide whether this is WAI or wont fix or fixing it.