Are the fees supposed to come out of your refund?

If the IRS is taking too long to send your refund or reduces it see.....
https://ttlc.intuit.com/community/payments/help/what-if-my-federal-refund-isn-t-enough-to-cover-my-t...

Then when the IRS does send your refund they won't take the fees out again.

And, Why you got charged,
https://ttlc.intuit.com/community/charges-and-fees/help/why-was-my-bank-account-auto-debited-for-tur...

You should have received about 4 emails asking for the fees. If you don't pay they will debit your account. You had to agree to it. Check your spam folder for emails.

Because you told them they could if the IRS took too long to process the return thus delaying the refund ... they sent you 4 emails to alert you  of the situation and the date of debit and how to get it deferred BEFORE they debited the account.   In the program when you choose to have the TT fees withheld from your refund you were presented with the contract twice and you had to agree to it twice.  Failure for you to read the contract you signed is on you.  

FAQ:  Why was my bank account auto-debited for the TurboTax fees?

https://ttlc.intuit.com/community/charges-and-fees/help/why-was-my-bank-account-auto-debited-for-tur...