Review your form 1040 lines 65 & 70 ... is that the correct amount you paid ? Or did you pay more?
When you prepared your final tax return, there is a place in turbotax to enter "tax payments paid with extension". Depending on which account(s) you used, your payment might or might not have carried over.
Download or print the PDF for your tax return and look at lines 64-74, that is the payment and refund calculation. Amount paid with extension is line 70. If that is correct, then follow it through to line 75, it could be that you owed more than you thought. If line 70 is blank, then your extension payment was not entered.
The good news is that the IRS will probably figure it out on their own and send you a refund for the double payment without you having to file a new form. You could try and file an amended return, but they take so long to process that it probably won't be any faster to get the double payment back (if you made one).