My employer contributes $200 per quarter to my HSA but has reported $6k the last two years. Why are they doing this and can I correct box 12 (W) to reflect the $800 and not $6000?
Under IRS regulations, all contributions made by payroll deduction, whether your voluntary contributions, or an employer match, are considered employer contributions and are reported on your W-2. The idea is that you agree to a voluntary salary reduction and your employer contributes the money.
If box 12 code W is the total of your voluntary payroll contributions plus your employer share that is correct. DO NOT add your contributions later in the program, that creates a double entry. You should only manually enter extra contributions you made on your own not through payroll.
If box 12 is not correct (it is more than the combined total of your employer match and your voluntary contributions) then you need to talk to your employer to get a corrected W-2.
No, you can't simply correct your W-2 form on your tax return.
You should ask your employer about this and if your W-2 form can be corrected.
It is possible that your employer is paying for your health insurance with the difference, but only your employer can explain what they are doing.