Are you comparing the tax on 1040 line 16 with the tax tables? Is line 16 less? That probably is not the reason for the IRS adjusting your refund.
It depends on what kind of income you have. There are like 7 different ways to figure the tax.
See the IRS worksheet on 1040 page 36 for how the tax is figured. Turbo Tax uses the same worksheet.
https://www.irs.gov/pub/irs-pdf/i1040gi.pdf
If you have capital gains or qualified dividends the tax is not taken from the tax table but is calculated separately from schedule D. The tax will be calculated on the Qualified Dividends and Capital Gain Tax Worksheet. It does not get filed with your return.
In the online version you need to save your return as a pdf file and include all worksheets to see it.
For the Desktop version you can switch to Forms Mode and open the worksheet to see it. Click Forms in the upper right (upper left for Mac) and look through the list and open the Qualified Dividends and Capital Gain Tax Worksheet.
You can probably tell because the tax on 1040 will be less than the Tax Table
https://ttlc.intuit.com/community/forms/help/form-1040-line-11-amount-is-less-than-standard-irs-tax-...
