I filed my taxes and gave permission to have the refund pay off the state tax due but I received a letter that the payment did not make and was charged with a penalty?

My federal tax return should have been applied to pay the state tax return. The letter from the Department of Revenue is rejecting the payment and are charging a high fee for this. Can I dispute the penalty? Why am I finding out much later after filing months ago now that I have relocated to a new state. That's rather suspicious that I did not receive notice when I was living in East Boston.