This has nothing to do with the retirement section not yet being available in step-by-step mode. The entries in forms mode that create the reporting of an excess-accumulation penalty are done directly in Part IX of Form 5329, so to get such a penalty being reported means that you made an incorrect entry there. Examine Form 5329.
The RMD entries on TurboTax's 1099-R forms serve only to indicate the amount that is ineligible for rollover. TurboTax has no way to determine the amount that you are required to have distributed. Your tax return only shows an insufficient amount distributed if you self-report the shortfall on Form 5329 Part IX.
