Your proof of payment is the canceled check, bank or credit card statement with amount paid and the Payee as either the IRS or the US Treasury.
Contact the IRS using the phone number on the notice and speak with an agent. You will need provide a copy of your proof of payment to the IRS.
Your only proof that you paid your tax due will be your own bank/credit card records. You did not pay "via TurboTax"-- you can indicate in the software that you want the tax due to be debited from your account by the IRS, but the IRS handles that--not TurboTax. If you entered a wrong account number etc. the IRS could not debit the account.
If your account shows that the payment was made then call the number on the IRS notice and sort it out with the IRS.
You cannot pay via TurboTax. You can provide your direct debt information on your tax return that goes to the IRS or by Credit Card that is depleted by a CC company that the IRS uses. Either way your proof of payment is your bank statement or Credit card statement.
How did you pay?