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You said you negated the 1099-MISC as illustrated in the answer above. 

Did you also then add that same amount in the Education Section as Scholarship income? You need to enter the amount of the 1099-MISC in the education section as scholarship not on W-2 or 1099.

"...return to the Education section and enter as Scholarship Income:

Enter under
Deductions & Credits
Education
Expenses and Scholarships (Form 1098-T)
Continue through the interview and enter the 1098-T if you have one, if not just ignore the screens asking about Form 1098-T and continue until you get to the "Did you Receive a Scholarship or Grant in (XXXX Tax Year)"

The program will say "Don't enter scholarships already reported on Form 1099" but in your situation, since you zeroed-out the 1099-MISC, ignore that warning and enter the amount."

When finished, you should see the 1099-MISC and the negative entry, BOTH,  on Schedule 1 Line 8z and the amount of the scholarship on Form 1098-T plus the amount of the 1099-MISC on Schedule 1 line 8r.

If the amount of scholarship from your Form 1098-T is working properly, delete Form 1099-MISC and reenter. If the program is still insisting the 1099-MISC is self-employment, it's how you're answering the questions when entering the 1099-MISC that is causing the issue. 

You can first try to edit the 1099-MISC. If that doesn't work, delete it and re-enter.

Please pay attention to the questions in that interview.

Enter the 1099-MISC as it was reported, Type "Scholarship" in for the description, Select "None of these apply" for uncommon situations, 

"NO" not like main job, 

Only got it in 2024,  

"NO" no intent to earn money, 

DONE

 These are TurboTax questions, not IRS questions. These need to be the answers to let TurboTax know it is not Self-Employment.

HERE is how to delete the form. 

So if the 1098-T is working fine and the scholarship income from that is flowing to schedule 1 line 8r you need to do THREE things with the 1099-MISC

1. Enter it and answer the questions as posted above

2. Enter the same amount as a negative number under "other income"

3. Enter the same amount as a positive number as "scholarship not on W-2 or 1099" in the Education section (the same section you entered the 1098-T)

At the end you will have 1099-MISC on Schedule 1 line 8z

Negative on Schedule 1 line 8z

Total scholarship amount on Schedule 1 line 8r

Scholarship on Schedule 1 line 8r can be used for IRA contribution