if entered correctly, an HSA contribution showing on your w-2 (box 12 code w) should show up on line 9 of form 8889. all amounts put in your HSA, even those taken on of your paycheck, are code "w". because your taxable wages in box 1 of your W-2 have been reduced by your contributions you get no deduction on your tax return for them. however, form 8889 is required. at this point you can do nothing. most likely the IRS will discover the code W on the W-2 and the missing 8889 and send you a notice. at that point follow the instructions in the notice.
