Found it online:
Oh yeah, I had a Glitch at Pokemon Go Fest. I bought one of the Great Boxes. The game lagged and bought as many as it could which ended up being three boxes. I was going to be like, Whatever.

, but I contacted customer support and they are working on fixing it. I was a bit slow to respond.
I hope they can return two of the boxes.
Chris bought one of the boxes and didn't have that problem.
Edit: They fixed it and I have my PokeCoins back! I'm amazed at how well that all went. I have had problems like this with some other games and they are just like, "Records show you did this so sucks to be you!" Well, not put so rudly but you get the idea.