If you mine a bee nest or a beehive with a silk touch enchanted tool, they are stacked in a separate inventory slot, although they all should have the same nbt properties (numbers of bees inside, honey level)

How to reproduce

Make sure you obtain those via crafting, commands or creative inventory so that you get the default ones (no bees inside, no honey filled) Switch to survival mode, then:

Mine a bee nest with a silk touch axe -> drops itself but stacks in another inventory slot 

Mine a bee nest with a regular axe -> drops nothing 

Mine a beehive with silk touch axe -> drops itself but stacks in another inventory slot 

Mine a beehive with a regular axe -> drops itself and stacks