The fees coming from your federal refund consist of the federal program cost + the state program cost + sales taxes (if any) + the refund processing fee + the paper check fee (if the direct deposit could not be made). The state/fed fee could be the same as the refund processing fee which may make it look like you paid it twice. If the IRS took to long to send the refund then you would have been charged for the fed/state fee earlier and then when the refund is finally released the bank fee is taken for their service.
