Your employer has the power to reclaim those funds under the rubric that they should have known that when they made the contributions, that you were not eligible. If they would do that and issue a corrected W-2 without the code W, that would be the simplest for you. So be nice when you ask your employer about this.
Otherwise you will have to tell TurboTax that you had an HSA so you can enter the HSA interview, then in the HSA interview tell TurboTax that you never had an HDHP coverage (which is how you describe having conflicting coverage).
TurboTax will declare the entire code W amount to be in excess, and add it to your Other Income. The good news is that the HSA custodian will send you a check for the amount of the excess.
Please tell me that you had this employer contribution stopped as of January 1st.
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