Normally this happens when you make changes after you filed so you accidentally changed the return ... did you start the amendment process by accident ? Is there a 1040X in the PDF ?
Not sure what exactly you looked at. TurboTax shows a summary that can net out the difference between a federal tax owed and a state refund--or vice versa. You have to look at the actual tax return forms to see how much you owe or how much your refund is. And your proof of payment is your own bank/credit card record. TurboTax never knows how, when or even if you paid your tax due.