You are missing the fact that when the IRS says the "employer" contribution, they mean both the amount that the employer contributes AND the amount that you contribute by payroll deduction. In short, the code W amount in box 12.
Why do they do this? Because these amounts are treated the same way. The entire code W amount is removed from Wages in boxes 1, 3, and 5 before your W-2 is ever printed.
That's why there is no HSA deduction for these dollars - because they were never in your income in the first place.
In any case, the code W amount is on line 9 (8889). Line 2 is only those dollars that you contributed directly to the HSA, not through your employer. These dollars do have a deduction - on line 13 on Schedule 1 (1040).
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