Did you make this extra contribution THROUGH your employer or not? Most taxpayers would have made this contribution directly to the HSA custodian. In this case, you would NOT ask for a corrected W-2, since your employer had nothing to do with the contribution.
Instead, you would get back into the HSA interview, and on the screen where it is headed "Let's enter [name] HSA contributions", enter this contribution in the second line where it reads, "Any contributions you personally made (not through your employer)".
Come back and tell us if my assumption is wrong.
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