I was not able to reproduce the symptom with either the CD/download version or the online version of TurboTax. When I created a tax return for someone age 33 with the only income being a Form 1099-R with an amount in box 1, the same amount in box 2a, no box 2b boxes marked, code U in box 7 and the IRA/SEP/SIMPLE box unmarked, Form 5329 was not produced.
Do you have any other Forms. 1099-R entered? There have been a few occasions over the years where TurboTax has had some bizarre interactions between Forms 1099-R, although all of those I'm aware of have been resolved.
