After you file

That's what I said in my first post.  Just keep waiting.  The IRS is taking a long time to process returns this year.  Why did you amend?  You should not have amended until the first return is done and you get the first refund.

 

Because Turbo Tax took the fees out of your bank account doesn't affect when the IRS will send the refund.  Only the IRS can tell you.

 

Since the IRS is taking too long to send your refund you still had to pay the fees in time.

 

See What if the IRS reduces your refund or delays it.

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.