To clarify, you are using TurboTax Online?
When we are opening tokens they open in TurboTax Desktop and in TurboTax Desktop you get follow-up questions for the inherited Roth IRA. But when I tested it in TurboTax Online I don't get the RMD questions for the inherited Roth IRA. When I recreate the entry of the two Form 1099-Rs in TurboTax Online I do not get a penalty on Form 5329.
Can you try one more time to delete the Form 1099-R for the Roth IRA and then go all the way through the retirement income interview. Then add the Form 1099-R for the Roth IRA again.
If you are still having issues you might need to switch to TurboTax Desktop: How do I switch from TurboTax Online to TurboTax Desktop?
@jfschultz
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