The explanation is that the total income shown on your return is a combination of your W-2 and 1099-R incomes along with any other income you may have reported on the return. Your tax is then calculated by reducing the total income by your deductions to arrive at your taxable income.
The tax withheld on your 1099-R may be correct, based on the withholding tables, but remember you are taxed on your taxable income, so you may still have had under withholding based on your combined total income.
