First would be to examine the pdf of your tax return with all worksheets to see that it includes Form 5329 showing the penalty calculation on the excess contribution and your limited Roth IRA contribution determined on the Roth IRA Contribution limit Worksheet (with the excess being the difference between the amount contributed and the limited amount). Assuming that these are present, you can then open the taxfile for the particular year in that year's version of the CD/download version of TurboTax and step through the Traditional and Roth IRA contribution section to see TurboTax's indication of the excess contribution.
Because the Roth IRA contribution limit is determined only after you have entered all items that go into determining your MAGI and have entered any traditional IRA contribution is TurboTax able to fully determine any excess Roth IRA contribution. If every section in TurboTax is visited in the prescribed sequence, TurboTax will be able to determine when you first visit the Traditional and Roth IRA contributions section that either you do not have an excess contribution or that you might have an excess contribution, depending on entries in the few remaining sections that follow that can produce additional above-the-line deductions (e.g., alimony paid) that would lower your MAGI.
