It is not unusual for your Form W2 to not match your paystubs - this is the main reason that we advise people to wait until they receive all of their forms before they file their tax returns. It is usually related to benefits provided by the employer that has an effect on your taxable income such as retirement plans or health insurance. There could also be a timing discrepancy depending on your pay cycle.
Of course, if something looks wildly off, then you may want to contact your employer/HR department/payroll office and inquire further.