Since you didn't pay tax on the money that ended up in the HSA, you don't get a deduction for this HSA contribution. It appears that the HSA is effectively being funded from the premiums paid by your employer (equivalent to a discount on the premiums paid by your employer and an HSA contribution by your employer), so I don't think that I see any problem reporting it as an HSA contribution made by your employer that was not reported on your W-2, resulting in it being included on Form 8889 line 9 instead of line 2 and no need to include it as miscellaneous income.
