How to fix being charged twice for in-app purchases already paid for and received?

For a while I was unable to install or update apps. The reasoning for this was revealed to me thanks to a customer service employee (Who I've forgotten the name of). I owe just under forty dollars for a bunch of pending in-app purchases. I said okay and thank you, and hung up as I had everything I needed. However, a while later, I looked at those pending purchases again just to confirm how much I owed, and I realized. Almost every pending purchase there is something I already purchased, was charged for, and have access to in the respective apps. I really do not understand why I am being charged again for something I already paid money for.

[Re-Titled by Moderator]

Original Title: App store says I owe money for In-App purchases I already bought and was charged for.