If you did not make a payment then you need to correct that in the program ... be aware that there will be an underpayment penalty added  AND  the IRS will now bill you for a late payment fee + interest after you file. 

To enter, change or delete a payment made with an extension request (Federal, State, Local) -

• Click on Federal Taxes (Personal using Home and Business)
• Click on Deductions and Credits
• Click on I'll choose what I work on (if shown)
• Scroll down to Estimates and Other Taxes Paid
• On Other Income Taxes, click on the start or update button

On the next screen select the type of extension payment made and click on the start or update button

Or enter federal extension payment in the Search box located in the upper right of the program screen. Click on Jump to federal extension payment