After you file

Filed my mother return by 5/17.  She gets a letter from IRS that she has not paid even though we Turbotax is set up for Direct Debit.  She paid by Check.  Now she have a letter saying "we misapplied payments, you still owe".  Money has left her account and now we are stuck calling the IRS.  What happened TurboTax????  Why didn't the direct debit work???