After you file

Oh man,  that was the wrong thing to do.  The bank will probably reject the deposit unless their name is on the account.

But anyway the fees are owed.  Hope you can get reimbursed from your friend.  Sounds like the IRS is taking too long to send their 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...  

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