There is most likely nothing you are doing wrong. The tax calculators, tax bracket calculations, and tax tables all calculate income tax based on ordinary income. They do not take into account items such as qualified dividends or capital gains that are taxed at a lower rate than ordinary income. If a portion of the total taxable income was due to qualified dividends or capital gains, then the overall tax will be less. How much less will depend on how much of the income is being taxed at a lower rate.
As suggested by user cr-stagg, you can see how the tax is calculated by taking a look at the Qualified Dividends and Capital Gains Worksheet.
@roninshawneeKS
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