Why am I being charged a separate transaction fee from the turbo tax fees?

We cannot see your fees.  Did you choose to have your TurboTax fees deducted from your federal refund?  If so, you have an extra refund processing fee of $39.99 ($44.99 in CA) for having a third party bank extract the fees from your refund and send you the rest.

How can I see my TurboTax  fees?   

https://ttlc.intuit.com/questions/2565973-how-do-i-review-my-fees-in-turbotax-online

If your TurboTax fees are higher than expected, you can reduce Remove Pay With Your Refund

• Remove Premium Services
• Remove MAX Defend & Restore
• Remove a state them by removing add-ons:
• Remove PLUS Help & Support

Are you referring to the convenience fee charged by the credit card processors on the IRS payment page? If so, TurboTax has no control of these fees. However, you can pay without fees by check or via IRS direct pay.