Normally, your pre-tax contributions (both your employer's if any and yours by a payroll deduction plan) will be listed on your W-2 in box 12 with a code of W.
It is not normal to repeat your HSA contributions in box 14 of your W-2.
I am concerned that the employer may have placed its contributions to your HSA in box 12 and your payroll deduction contributions in box 14 or vice-versa. If so, this would be wrong.
Both your employer's contributions to your HSA and your contributions by means of a payroll deduction plan should not only be reported in box 12 with a code of W, but the total of these two types of contributions should be removed from Wages in boxes 1, 3, and 5 since HSA contributions are not subject to federal income tax, Social Security tax, and Medicare tax.
Box 14 is usually used by employers to note items of interest to employees and don't affect your tax return. HSA contributions would not normally go here.
You should go to your employer and ask if the HSA contributions were correctly listed on your W-2.
