Your question doesn’t make sense as stated. Scholarships and Pell grants are taxable income if they exceed the cost of tuition (for example, amounts used to pay for room and board.) However, there is no reason why the IRS should get scholarships and W-2 income confused if you e-file.
Scholarship income that is more than the cost of tuition would be reported on line 1 with “SCH” next to it. If you also have wages from W-2s, that will also be included on line 1.
I would start by making an online account at the IRS and obtaining copies of your 2019 tax return transcript and wage and income transcripts. See if the IRS has income on file for you that does not match what you reported.