Even if the money is reflected on the return did it ever get paid ? Do you have a cancelled check or bank statement showing anything was actually paid with the extension ?
If you do not have a receipt for the payment then it never happened ... so the IRS is correct.
If you did pay then :
Take a look at your account transcript on the IRS web site ... do they have a payment listed ? https://www.irs.gov/payments/view-your-tax-account
You could try to call ... may never get thru but you can try.
Or you can amend the return ... could take 6 months or more to process.
Or you can wait and see if the IRS every catches this overpayment and sends it to you.
