You did not "already pay tax". What you paid was only withholding, an estimate of the tax due. No piece of income is taxed individually. All your income, including pension plan distributions, is added together at tax filing time. The tax is calculated on that total (after adjustments, deductions, exemptions and credits). Then withholding is subtracted to determine if you owe more or get a refund.
As the other answer said, check the IRS notice to see if they gave you credit for the withholding (box 4 of the 2018 form 1099-R).
The IRS calculations are not always correct. Recalculating your tax to confirm the IRS billing is recommended. If you come up with something different, you should submit an amended return.
