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After you file
@smotyka wrote "I submitted my taxes via E File via Turbo Tax Premier which I had already purchased with the option to have my charges subtracted from my refund of which I was charged $40.00."
You didn't mention exactly what product you used, but I'll assume it was Online TurboTax. Hopefully, you didn't buy a CD/download product, but then used Online TurboTax by mistake. We have seen that happen before. This answer is going to assume you used Online TurboTax for everything.
When you choose to pay out of the Federal refund, you're not actually paying at the time of efiling; it's not an upfront payment. You are postponing it to be taken out when your refund arrives from the IRS at SBTPG's bank. So it's not clear what you mean by "already purchased."
There is a 39.99 service fee when one chooses that option to pay out of the Federal refund. It's paid at SBTPG when they process the refund.
Your situation is not clear, and it can't be resolved in this user community forum anyway. Here's how you can phone TurboTax Support, and they can question you to see what you are experiencing. If you were actually double-charged, they should be able to fix it.
FAQ: What is the TurboTax phone number?
https://ttlc.intuit.com/community/using-turbotax/help/what-is-the-turbotax-phone-number/00/25632
In those FAQ instructions, if you're using Online TurboTax, you should first try the "Talk to a Specialist" method which may route you to the correct department. If you have to enter some keywords, say billing issue.. It also shows a phone number to use, if necessary.