The IRS has asked me to explain the tax withholdings on my 1040. Where can I check what numbers TT added up to fill in the information on line 12 F1040?

@tde , if you cannot see the actual form  ( and therefore confirm that  the line 13 is in error ) , you can :

(a) write to the IRS to explain what took place -- that it is an error  of  putting the amount on the wrong line  but the total amount of refund expected is still correct  --- on the form they sent you there is an area to disagree with them and explain why -- that is where you put your explanation

(b) Prepare an amended  1040 on TurboTax and send this along with the answer to IRS query.

My pref  and strong suggestion is to follow  option (a) since IRS is already asking for explanation.   You should be getting a resolution soon thereafter.

Good Luck

If this is for the 2019 return and you used the ONLINE program  then you may still be able to log in and look at the return entries and download a PDF with all the worksheets before the 6 week blackout period while the returns are moved and archived.

Just make sure you don't change anything ... look but don't touch.

• Log in and at the Tax Home or in the section "Your Tax Returns & Documents" for 2019, look for a link "Add a State."
• Click on "Add a State."  (you don't really add one.  That's just to open your return back up.)
• After the return is open, click in the left menu column on TAX TOOLS, then PRINT CENTER.
• Then choose "Print, save, view this year's return."
• The next screen should offer some options:  "Just my tax returns", or "include government worksheets (optional)", or "include government and TurboTax worksheets (optional.)"
• See if one of those PDFs has what you need.

If you want to touch then download the amendment program and the .taxfile. 

DID you really apply the taxes from 2018 ?  If the IRS sent a notice it would seem you did not do so.  Look at your 2018 return form 1040 line 21 ... did you indicate the refund was to be applied ?   

I'm having trouble finding lines 12 or 13 having anything doing with withholding or taxes paid on an IRS form 1040 for 2019...or any of the previous 3 tax years. 

.......should be lines 17 & 18d of the 2019 IRS/Federal form 1040.....OR maybe you are talking about some state form 1040, since some states use "1040" as a part of their form names too  (Iowa uses IA-1040)

______________________________________________________

In either case...check the following

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One place to check the TTX forms for where you entered the refund from 2018 applied to 2019 taxes (if those are the years you are dealing with)

If you have saved a PDF copy...for your records, with all forms and worksheets (not just the bare tax return)...in that PDF file, there is a Tax Payments Worksheet.  

a)  Total of all W-2 withholding is on line 10 of that worksheet.

b)  The 2018 refund carried to 2019 should be on line 6 of that worksheet.   

But.....IF you entered it at some other location, you should see where it is on that worksheet.
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For example: 

c)  If you accidentally entered that 2018 carryover during the interview as "Other withholding", then it will show up on one of lines 18a,b, or c on that worksheet.  And for a Federal form 1040 , it will total into line 17 of the actual Federal Form 1040.   (but if you talking about a state form and state refund carryover from 2018 in the State column of  that Tax Payments worksheet...then it goes to whatever line is appropriate on the state form)

d) IF you properly entered the Federal 2018 carryover to 2019 in the tax software, then that shows up on line 6 of the worksheet......and that would then add-in to , line 18d on the Federal/IRS form 1040, (along with a couple other estimated payment types, but not withholding).  Or if in the state column for line 6 on the worksheet....that goes to the appropriate place on your state form.

Thank you!

@streamtrain - thank you for the detailed answer. I should have been more specific, it was form 1040-X (amended return), which might explain the difference in lines?

@everyone, the difference was caused by the additional medicare tax on the W2 which was added on top federal income tax withheld from the W2. I didn't realize that I had to add that as well.

Additional medicare tax ?  where did it show up ? or you talking about that TurboTax computed  your medicare tax as different from that shown on your W-2 and therefore the diff. to reconciled ?  Did your employer make an error?