Yes if you selected to have the fees deducted from your refund. 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-turbotax-fees
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/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.