Since you originally made no mention of this being a question about past behavior, I assumed that this is behavior that you are presently seeing by making entries into TurboTax. Since you are referring to behavior that you are remembering from preparing some past year's tax return with the online version of TurboTax, examine the Roth IRA Contribution Limit Worksheet and Form 5329 contained in the pdf of all forms and worksheets that you downloaded after preparing your tax return.
Also, the refund/balance due calculation is relatively meaningless until you've completed all entries for your tax return. For example, entering a Roth IRA contribution before you enter your compensation would certainly result in TurboTax seeing the contribution as an excess contribution. In this case the penalty would disappear when you enter your compensation, provided that that compensation did not put you over the MAGI limit for your filing status and the compensation was not excluded foreign earned income.
