You are correct. Employee contributions to an HSA through a cafeteria plan are not included on Line 2 of the form 8889. That is because they are included on Line 9 (see instruction here) of the form 8889 by way of a Code W in Box 12 on your W2 as @RalphH1 shared.
Whether on line 2 or line 9 if the total exceeds the limitation, it is excess contributions. For a self-only HSA that limitation is $3650; for a Family HSA it is $7300.
If an amount on Line 2 does not cause the total contribution to exceed the limitation, it becomes a deduction on your tax return. An amount on Line 9 has already been excluded from taxable wages as reported in box 1 of your W2.
As @RalphH1 explained to change the nature of the box 12 amount, a corrected W2c from your employer is needed; otherwise if you have excess contributions you need to work with your HSA servicer to get that excess removed before the filing deadline (including extensions). You may need to put in an extension to get this accomplished.
@ryan-hamel
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