This sounds like something that you would report as miscellaneous income and as a personal HSA contribution. The deduction for the HSA contribution would offset the miscellaneous income so there would be no change in your AGI, but the entry of the HSA contribution is necessary for Form 8889 to be prepared correctly.
Alternatively you could indicate that your employer told you about this amount of HSA contribution and that the employer did not include it on your W-2. The taxable result would be the same as above but the reporting of the amount would be on Form 8889 line 9 instead of line 2 and there would be no miscellaneous income to report or any HSA deduction.
