Where is it telling you that you are being penalized?
Are you sure it's not just a 20% tax being applied? The income is taxable if it is not a ROTH account.
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If a penalty is being applied, it would show on Schedule 2, Line 6.....but would be 10% of the distribution for that 1099-R.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*