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If you choose to pay your fees from your federal refund, then TurboTax will show that the fees are "paid" ----but they are not really paid until the IRS issues your refund and the third party bank extracts the fee and sends you the rest.
In the event that there is a too-long delay in processing by the IRS, you agreed to allow the fees to be taken out of your account even before the refund is issued.
You signed an agreement that says TT can withdraw its fees from your account. TurboTax would have sent several emails to you before they took the money out of your account.
https://ttlc.intuit.com/questions/1901364-why-was-my-bank-account-auto-debited-for-turbotax-fees
Only the IRS can tell you the reason for the delay in issuing your refund, but lots of folks have been waiting for months.
Tax Season Refund Frequently Asked Questions | Internal Revenue Service (irs.gov)
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