Is the amount reported in Box 14 by any chance? If so, you need to know if the deductions were done pre-tax or post-tax and you may need a corrected W-2. The amount that both you and your employer contributed to your HSA account should be reflected in Box 12 with a code W. These amounts are not taxed and should not be included in your gross income in Box 1. Where you enter them and how it affects your tax return is dependent on how the deductions were handled by your employer. The first box says 0 because there is no entry with a code W in box 12. And if they were deducted post-tax, then you need to take a deduction as those amounts are not taxable, but only your employer is going to be able to answer that for you.
Are you sure these were HSA contributions and not HRA or FSA deductions? In order to contribute to a health savings account (HSA), you must be enrolled in a high deductible health plan (HDHP). If they are not HSA contributions, then you don't need to go through that section. @jessica293
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