The amounts in box 1 and box 3 of your W-2 will be different if you had a pre-tax deduction. Some pre-tax deductions reduce your taxable income (box 1) and your social security income (box 3). Other pre-tax deductions only reduce your taxable income (box 1). If you have a deduction that only reduces your taxable income then the amounts in box 1 and box 3 will be different. Generally these pre-tax deductions are listed in either box 12 or box 14. You can calculate the difference between box 1 and box 3 and see if the amount matches any amounts in box 12 or box 14. If they do not you can also contact your employer to ask which deductions are being deducted from your federal income and not your social security income.
