I ran into a weird TurboTax/IRS timing issue, so I’m posting this as a warning.
I filed my original federal return on March 17. After the e-file was accepted, I realized I had missed reporting some interest income. I filed an amended return through TurboTax on March 22. The amendment created additional tax due, so I paid that amended tax amount through TurboTax the same day, well before the April 15 deadline.
My original refund did not come until April 22.
Here’s the problem: the IRS had not processed the amended return yet. So their system still treated my original return as showing the original refund. I guess the amended tax payment I made was sitting on my IRS account as an extra payment or credit. When the IRS issued my original refund, they included that amended tax payment in the refund and sent it back to me. I did not notice this.
Today, I received a balance-due letter saying I owed the amended tax amount they had just refunded back to me, plus penalty and interest.
I called the IRS to confirm (1h 30m), and the letter was correct. The math added up, so I made the payment again.
My takeaway is to not make mistakes that require amendments. lol.
But also, if you file an amended return that creates additional tax due before your original refund is issued, compare the actual refund deposit against the original refund amount you expected.
If the refund is higher than expected by roughly the amount of your amended payment, the IRS may have refunded your amended payment back to you before processing the amendment. Handle it asap. You will still probably be penalized.
I wish TurboTax warned me about this timing issue.