You don't provide enough information.
On the question of how did this happen, we would need to know what year, your other income, and whether you even entered the Roth IRA. Roth contributions are not required to be entered on your tax return. Turbotax asks for the amount to give you proper advice, but you might not have entered it.
On the question of how to fix it, we need to know what year or years you made the contribution, why you think were ineligible, whether you are eligible this year, did you make any IRA contributions this year, and whether or not you ever filed form 5329 to report the problem and pay a penalty.
Also, please note that workplace plans (401k, 403b, etc.) are not IRAs, and the rules are different. You are almost always eligible to contribute to a Roth account in a workplace plan even if you are not eligible to contribute to an IRA.
