If multiple bees leave a beehive block at the exact same time, the honey level only increases by 1.  This is most apparent at the start of a new day, when all the bees leave their hives at the same time in the morning.

Steps to reproduce:

1: Build a small enclosed space that has a flower, a beehive, and 3 bees.

2: Wait for the bees pollinate and return to their hive.

3: Set the time to night.

4: Wait for morning with the debug screen on and the cursor hovering over the beehive.

5: Watch as the honey level only increases by 1 when all three bees leave their hive.