So, I was looking through the research list for the recipes out of curiosity and came across the recipe for an energy drink. What didn't make sense though was the material it needed. It needed a Squad Energy Box to make ONE energy drink, and yet the Squad Energy Box needed three energy drinks to make.

The latter I can understand, but why would you need that many to make the former?

You must have read it wrong; it takes 3 Energy Drinks to craft one Squad Energy Pack (which saves you 1 Energy Drink as Squad Energy Packs replenish the health of 4 pets) and deconstructing a Squad Energy Pack produces 3 Energy Drinks.

What I mean to say is that for some reason, the energy drink requires a squad energy box to make it. Needing three energy drinks to make the squad box I can understand, but not the needing a squad energy box to make a single neergy box.

I just double checked to see if I had seen it wrong, but its still the same. 

Energy Drinks

The recipe says Energy Drinks, and it takes 1 Squad Energy Pack to make. What you are doing is essentially taking the pack apart to get the individual Energy Drinks from it.

So by taking the pack apart, are you getting four energy drinks or just the one?

You do not get 4, you get 3. Crafting a Squad Energy Pack only takes 3 Energy Drinks and so you only get 3 when you use it to craft Energy Drinks. Using a Squad Energy Pack is a bundle deal - use 3 get the 4th free. Understand?

If you go to the Premium Shop you can see that an Energy Drink costs 5 gold while a Squad Energy Pack costs 15. Buying 3 Energy Drinks costs as much as buying a Squad Energy Pack although the pack can be used on an extra pet.