Did you make a payment with the extension? It should have shown up on 1040 line 70. Is it there? And you have proof it was taken out of your bank account? Maybe it was applied to the wrong type of payment. Like to a 2017 estimated payment instead of a 2016 tax due. Is the bill just for more interest or penalty? That is common for them to send a bill for interest depending on when they got your payment.
