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.  Then when the IRS sends the refund they won't take the fees out again.