@abaptista
I suggest that you make another pass at your payroll people to explain to them that the use of code W in this case is wrong.
A Health Savings Account is a unique financial instrument that is well defined in IRS Pub 969 on page 2: "A Health Savings Account (HSA) is a tax-exempt trust or custodial account you set up with a qualified HSA trustee to pay or reimburse certain medical expenses you incur. You must be an eligible individual to qualify for an HSA."
Did you employer help you set up such an account? If so, ask them where it is, and then note that the account belongs to YOU, not your employer, and that they have no control over it outside of possibly making some contributions to it.
The instructions for the W-2, W-3 (quoted in the thread above) clearly state that code W is only for use for contributions to an HSA.
The fact that contributions to an HSA can be part of a Section 125 plan does not justify using code W.
If your employer refuses to correct your W-2, then I suggest you take the following steps:
1. When you enter your W-2 into TurboTax, don't enter the code W or its corresponding dollar amount at all.
2. This will make your return correct in the sense that you will not have a form 8889 attached, since you don't have an HSA.
3. Keep detailed copies of these comments with your W-2 in your tax files in case the IRS asks, as they may when they see that your copy of the W-2 does not match the copy that the company sent them.
It is not common for me to suggest that you alter your W-2, but if you don't, your return will be materially wrong, so I view this as the lesser of two evils.
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