2023 Amended Tax Return - changing filing status

My husband and individually filed our 2023 1040 original tax returns each with the filing status of Married Filing Separately.  He received a refund of $9779.00 and I received a refund of $17.

 

We subsequently filed the 2023 1040X Amended return this past April 2025.  We filed it as amending my return, with a change in tax status to Married Filing Jointly.  In the Amended return, TurboTax Desktop Premier placed my married filing single refund  ($17) on line 18, and calculated a refund of $3,307.00.  It did not ask for my husband's refund entry as I recall.

 

It took about 17 weeks for the IRS to contact us saying we had to show proof of withheld taxes, we submitted that information, and now 20 weeks since the 1040X filing it says we owe actually owe the amount of his refund, plus interest and penalties of course.

 

In researching through AI, it appears that several references say that past refunds are "settled transactions" and that the IRS ignores refunds from the original tax returns.  

 

Can you clarify if TurboTax appears to be calculating the 1040X correctly in this instance.  Thanks very much,

 

Summary:

Original returns: 

Husband's 2023 1040 - MFS - refund of $9,779  Filed April 2024. Prepared on TurboTax Online;

My 2023 1040SR MFS - refund of $17 - e-Filed  April 2024. Prepared on TurboTax Desktop Premier.

Amended Return:

2023 1040X for my return- filing status changed to MFJ, with my husband's tax information combined with mine.  Refund claimed $3307.  Prepared and e-filed April 2025 with TurboTax Desktop Premier