You aren't being charged twice. If you chose to pay the TurboTax fees out of your Federal refund, then once the IRS offset your refund, it sounds like there wasn't enough left to pay the TurboTax fees.
See this FAQ on that issue:
FAQ:
What if my federal refund isn't enough to cover my TurboTax fees?
https://ttlc.intuit.com/replies/4169801
