Additional $39.99 fee charged --- sounds like you opted to choose the totally optional service to have your fees deducted from your refund.
Use your credit card instead.
There are at least 2 different screens that ask you to confirm you opted to use (and pay for) that service.
If you have not yet filed your return, you can remove the OPTIONAL Refund Processing Service fees and pay with your credit card:
https://ttlc.intuit.com/questions/1900517-how-do-i-remove-the-refund-processing-service
Here's help reviewing your TurboTax fees:
https://ttlc.intuit.com/replies/4202093
Why was I charged twice:
Here is some information about seeing 2 identical charges:
https://ttlc.intuit.com/replies/3300086
"If you see two identical charges (down to the penny) in your online statement, one of them is probably a temporary authorization as opposed to an actual charge or debit."
NOT an accurate statement. TTax has numerous services and options that have identical prices ---(down to the penny).