The same thing happened to me. I don't understand the details of why, but for some reason the form input filled out the underlying tax form wrong. If you go to the form (8889-T) itself using the 'Forms' button, you will probably see in sections 1 and 3 that the boxes to indicate coverage under a HDHP (high deductible health plan) were not checked, thereby making your HSA contributions non-deductible. I compared to my forms from last year. and made it look the same, because nothing has changed in my case. That fixed it, and showed my whole contribution as deductible on line 13 (HSA deduction). Hope this helps!
