You must resolve that with your employer. Amounts contributed by you or your employer are considered "employer" contributions under the tax code, and are reported in box 12 with code W, and should be subtracted from your gross income in boxes 1, 3 and 5. If your employer did not reduce boxes 1, 3 and 5, you need to get your employer to issue a corrected W-2.
Be aware, however, that while a 401(k) is only subtracted from box 1 (because those wages are still subject to social security and medicare tax), HSA contributions are exempt from medicare and social security tax as well, so will reduce boxes 1, 3 and 5. So you can't just compare box 1 and 3, you need to compare boxes 1, 3 and 5 against your pay stubs.
