When drinking a honey bottle, the "Times used" section in statistics will increase by two instead of one. It is also the same for scoreboard objectives. This could also be related to the fact that when you drink/eat an item that returns and item (Water bottles and stews, etc) it plays the armor equipping sound, which also counts as an item used in the **armor statistic menu.

Steps to recreate:

1. Drink a honey bottle (Or for further testing, any food item that returns and item such as stew)
2. Go to the statistic menu, you will see that the times used variable increases by two instead of one.
3. You can also create your own scoreboard objective based on the usage of these items to see that the scoreboard objective points will increase by two.