IRS credited my estimated taxes twice! How does this happen with TT?

I just got a letter from IRS saying:

"We changed your 2021 form 1040 to match our record of your estimated tax payments, credits, applied from another year, and/or payments received with an extension to file. As a result you are due a refund of $3658."

 

This amount was paid in October 2021 as a estimated pre-payment tax.  I used TT Business sIRS, TT and my calculations show total tax due for 2021 was $7685.  IRS says I paid them $11,343.  They added $3658 twice ($37 from a 1099, $3658 from estimated tax payment, $3658 from schedule 3 which does not exist in my 1040 forms, and $3990).

 

The AGI and TI match exactly. Tax due match. They say there was estimated tax payment from form 1040 line 26 Sch 3 line 10 for $3658.  I didn't submit this form. It was not part of the TT documents. My estimated prepayment was entered on line 25d of the 1040.

 

How do they (IRS)  add a schedule 3 form and credit estimated prepayment amount twice?