All contributions made through payroll deductions are listed as code W, employer contributions, regardless of whether the contribution came from the employer or the employee.
It's treated as coming "from employment." and it's excluded from your wages in box 1(pre-tax). You can't deduct the $2500 that your wife contributed, as it's already been excluded from her income.
If she contributed an additional amount (after tax) on her own, you would enter that as an additional contribution.
All contributions made through payroll deductions are listed as code W, employer contributions, regardless of whether the contribution came from the employer or the employee.
It's treated as coming "from employment." and it's excluded from your wages in box 1(pre-tax). You can't deduct the $2500 that your wife contributed, as it's already been excluded from her income.
If she contributed an additional amount (after tax) on her own, you would enter that as an additional contribution.
The problem is the HSA contributions were not deducted from Box 1 wages, only 401(K) contributions were deducted from Box 1 wages. I have e-mailed her payroll department to check on their recommendation or to issue a corrected W2.
Your wife's HSA contributions, if they are part of an employer "cafeteria plan" would be exempt from both Federal taxes and Social Security, so it wouldn't be in box 3. See page 11 of these instructions:<a rel="nofollow" target="_blank" href="https://www.irs.gov/pub/irs-pdf/iw2w3.pdf">https://www.irs.gov/pub/irs-pdf/iw2w3.pdf</a>