I'm thinking that what's going on here for everyone is that you have entered your contributions, but you need to also enter the distributions from those contributions which were used for medical expenses during the year. If And portion of the pre-taxed HSA contributions that are not used to pay your actual medical expenses during the year and/or by the tax return due date revert back to the taxable wages classification.
Also for future reference, as others have said, these employer/employee type contributions will not show up as part of your wages on your W-2, but if you look at your final, full detail payroll check stub/summary sheet, you will see the higher full wage amount that includes your HSA contributions amount; as well as, the actual taxable wages amount that carries over to the W-2, boxes 1, 3, and 5.
