TurboTax does not make any tax payments. You never make a payment "through TurboTax." TurboTax just sends the bank information that you enter to the IRS. The IRS debits the money from your bank account. There is no way that any glitch in TurboTax could have applied your payment to the wrong year.
But it's not clear whether the IRS messed up or you messed up, because it's not clear what "ran the process again" means. You could not have filed another tax return, and you could not have made the payment through TurboTax. How exactly did you make the payment that went through on April 28?
If you used Direct Pay on the IRS web site, you had to select whether it was for a balance due or for estimated tax (among other possibilities), and you had to designate the year. Direct Pay would not let you select 2023 for a balance due. If you selected estimated tax, it would automatically select 2023. If you have your Direct Pay confirmation number you could use Look Up Payment to see how the payment was designated.
