When you signed up for Pay with Refund, you agreed to let TT takes its fees if your refund was delayed beyond a certain point, so that is apparently what happened. But TT notifies you first.
Your fee payment will be taken from your refund, after your refund processes. Your refund is sent to a third party to process the fee payment then the balance is direct deposited to your deposit account on file with TurboTax. If there is a probably with your refund, TurboTax will send you a letter indicating they are taking the fees from your deposit account on file. This will not happen if your return is still processing with the IRS, and only if your refund is not enough to cover your TurboTax fees.