Sounds like the IRS is taking too long to send your refund.  See What if the IRS reduces your refund or delays it.
https://ttlc.intuit.com/questions/2552376-what-if-my-federal-refund-isn-t-enough-to-cover-my-turbota...  

And, Why you got charged,
https://ttlc.intuit.com/replies/3302146

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

https://ttlc.intuit.com/questions/1901364-why-was-my-bank-account-auto-debited-for-turbotax-fees