The IRS instructions page 9, explain that Code W in box 12 is for HSA contributions. Contributions are funds that you (and your employer if they funded some) elected to contribute to your HSA account on a pre-tax basis. Code W is only used for HSA contributions.
The statement, "Code "W" is everything that you have paid towards your HSA plan as a deduction, not a contribution to an HSA since you did not have an actual HSA account that you were contributing to" is incorrect.
If you had a Sec. 125 plan where you paid for your insurance as a pre-tax deduction, the code for Box 12 is DD. Your employer is confusing all pre-tax items as being coded W, which is simply not the case.
As others have said previously, your employer needs to provide a corrected W-2.
IRS W-2 Form Instructions
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