This question has only been partially answered and the topic is found in multiple posts. I've spent several hours now with help desks between the IRS online payment service, TurboTax and the IRS themselves. I would appreciate it if TurboTax Accountants review this post and provide a comprehensive answer on both why this happens but also how to avoid it. TurboTax should also review the customer experience for extensions because something is broken there.
Situation: I submitted the payment online using the IRS guidance and link. When I did that, there was no option to select "File as extension", as suggested in the instructions. There is also no option to add a note to say it is related to an extension. The Form 4868 says that once you make a payment, an extension will automatically be filed and that you should receive a confirmation.
Complication: I received a payment confirmation, but no confirmation that the extension was approved. I was in limbo wondering if the extension was filed or approved. As such, I went back into TurboTax and filed an extension. I received confirmation that it was filed, but then later it was rejected by the IRS. The instructions from TurboTax say to try again, which I did with the same outcome.
Resolution: My only guess is that submitting the payment did in fact trigger an automatic extension by the IRS. After a long time on the phone with the IRS, they confirmed that they saw three requests for the extension, which seems to point to the fact that the payment did trigger an automatic extension (because I only tried twice on TurboTax). That is contrary to what the Form 4868 says or even the IRS website, which again says to "if you use an electronic payment method and indicate the payment is for an extension, you don’t have to file Form 4868". That was not even possible with the online payment provider (ACI in my case).
If this happens to you, you can try to call the IRS to ensure the extension was accepted. I waited until tax day so IRS support was backed up and not an option, so I got my answer the day after. NOTE: There is an article that said if your extension is rejected you print and send Form 4868 via mail but that it needs to be postmarked by April 20th.
I did notice after-the-fact that if you select "Other Taxes" on the ACI online payment site you will see a "Pay Extension" option, but it was not obvious at all because it is in a different section and kind of buried. Using that may prevent the problem going forward.
Another way to avoid this error going forward may be to just submit the payment of taxes and the extension both through TurboTax, and not use the IRS site.
Hope this helps some other frustrated tax payer!
Below is the exact mail from TurboTax. Despite mentioning they will help resolve, TurboTax did not help resolve:
"This happens from time to time, but we’ll help you fix it.
What happened?
R0000-902-01 - Taxpayer TIN in the Return Header must not be the same as a TIN of a previously accepted electronic return for the return type and tax period indicated in the tax return.
What does this mean?
In most cases, you just need to submit a new extension application before the filing deadline."
