Bees can duplicate entities when they enter then leave a hive. 
This issue can only occur when a bee is spawned with passengers.

This is related to MC-159441; this ticket was made at request.

How to Reproduce:

• Summon a bee with passengers.
  Example: Boat riding a bee. Mainly because there isn't any controlling AI or momentum, and the solid hitbox makes it obvious if it has duplicated, despite being invisible.

  /summon bee ~ ~ ~ {Passengers:[{id:boat}]}

• Place down a hive and flower for it to go in and pollinate.
• Wait for the bee to pollinate and go to its hive.
• Use the following command on the hive.

  /data get block X Y Z

• Note how there's passenger data.
• Wait for the bee to come out of its hive.
• Note: Some entities don't duplicate, or appear to not duplicate. Those with solid hitboxes, ie. boats or shulkers, can generally be used to tell if it has duplicated.
  The UUID of the passengers may prevent it from persisting if multiple are present at once, which means you may need to kill the entities to have any duplication across saving.
  The boat is one of those that appear to not duplicate, but its hitbox can be found.