So did the IRS not take into consideration qualified dividends when they calculated my tax amount?
If I am interpreting things correctly (and I may not be) the IRS hasn't "said" anything yet. You're getting your figure from the tax tables - not from the IRS directly. The tax tables are basically for W-2 income, and the tax tables do not take into account things that may be taxed differently or at a different rate. So if you have things like qualified dividends, the tax tables are of no use for that income.
