Note that by not including your spouse's HSA payroll deductions in the W-2 Box 12 code W amount, that your spouse's employer may be overcollecting on your spouse's Social Security and Medicare taxes as well.
Well, let me put it this way: HSA contributions made through the employer (whether from the employer or through payroll deduction) are not subject to federal income tax OR Social Security tax OR Medicare tax. This the code W amount should have been removed from Boxes 1, 3, and 5 on her W-2 before it was even printed. How can you tell? You can't because unlike a 401(k) contribution that is removed only from Box 1, the HSA contributions are removed from all three boxes that show Wages. In short, you have to ask the payroll department.
In your case where payroll has apparently messed up on the Code W amount, there is a workaround if they removed the correct amount from Wages in Boxes 1, 3, and 5. In this case, you would go to Deductions & Credits->Medical->HSA, MSA Contributions and click Start or Revisit. Go through the HSA interview until you see this screen: "Did your employer tell you about any other contributions?"
Click "Yes" and you will see three additional lines appear. Enter the amount of your wife's payroll contributions that were NOT in Box 12 on the W-2 with a code of W on this line: "Employer and payroll contributions not reported in box 12 of your W-2".
But if your employer did not add your wife's payroll contributions to the code W amount NOR did they remove the same amount from Wages in Boxes 1, 3, and 5 (as I said, you will have to ask them), then they have really fouled up your W-2. And, unfortunately, filing your return with the W-2 information as is with the payroll amount added to "Employer and payroll contributions not reported in box 12 of your W-2" will make your federal income tax (and presumably your state income tax) correct, but the Social Security and Medicare tax collected will still be wrong and only your employer can fix this by updating their reports to the IRS and SSA (and refunding the difference to your wife). This is why getting a corrected W-2 is ultimately the right answer in this latter case.
Well, the first thing you want to do is to ask payroll (1) why did they not add your wife's payroll amount to the code W amount? and (2) did they remove the correct amount (employer AND payroll contributions) from Wages in Boxes 1, 3, and 5 on the W-2? Their answers will determine how you proceed.
