The first thing I would suggest is to double check your Pay-Stub and make sure it is actually Federal Income Tax Withholding you are looking at and not taxes withheld for Social Security, Medicare, or State Tax Withholding.
If you find that you are correct and there was Federal Income Tax Withholding from your pay that was not reported on your Form W-2 Box 2, you should immediately contact your Employer and have them issue you a corrected W-2C.