Did you enter a 1099-R? The 5329 form is for additional taxes on qualified plans. I suggest you delete the 1099-R and re-enter to remove the penalty that is on 5329. That section was recently updated to correct an issue with the RMDs.
How to delete forms in TurboTax Online
How to delete forms in TurboTax Desktop
Where do I enter a 1099-R?
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