After you file

Did they charge you the whole tax due?  Or just penalties and interest?  

If the bank rejected the payment better call the bank and double check the routing and account number you entered.  Or if the payment did come out of you account maybe the IRS is billing you for an underpayment payment penalty for owing too much?  Did you have an amount on 1040 line 38?  

The amount Turbo Tax calculates on your 1040 line 38 is only an estimate.  Turbo Tax can not figure it accurately because they don't know exactly when the IRS or state will get your return and tax due payment.  It's very common and normal and expected for the IRS or state to bill you for more or send you a refund.