No. Don't change the amounts entered on the W-2.
If the employer accidentally commingled the contributions to your HSA (which is code "W" in box 12 of the W-2) with premiums paid for your HDHP health insurance (which is code "DD" in box 12 of the W-2), then the employer needs to issue you a "Corrected" W-2.
This is because in the situation you have described, that you have likely not over-contributed to the HSA, but since the IRS has gotten a copy of this W-2, the IRS will think that you have. Contact the HR/Payroll department and ask them to correct the W-2 and to send it to you (and copy the IRS). Don't file until they do this.
