A 39.99 fee at this point in time is most likely a service fee for choosing to pay your TurboTax fees out of the Federal refund. That is handled by a third party who opens a temporary bank account in your name, receives a Federal refund from the IRS, subtracts the fees, then sends the rest on to your bank (or card) in a second deposit. Then the third party closes your temporary bank account. Did you use that service?
Are you using Online Premier? If so, the Federal return is 79.99, and the state return is 44.99.
If you chose to pay the TurboTax fees out of the Federal refund, there is an additional 39.99 service fee (44.99 for California filers.)
If you chose that method and have not yet filed, here's how to remove it and pay upfront with credit/debit card or a prepaid debit card you can buy in a store. If you already efiled, and if your efiled return is rejected, you may be able to remove it then as well prior to resubmitting.
Filers in states except California:
https://ttlc.intuit.com/questions/1900517-how-do-i-remove-the-refund-processing-service
California filers (where that refund processing option is part of "Premium Services.")
https://ttlc.intuit.com/questions/2154391-how-do-i-remove-the-premium-services-fee
