If the IRS sent you a letter saying you owe then you are not getting a refund anymore. They changed your return. So there is no refund to take the fees out of.
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...
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.
