I agree that based on what you have said, it doesn't make sense.
If anything, they should have INCREASED the amount (they paid you for Social Security in Box 4 of the W-2, but then when they realized that wasn't necessary, they reallocated that payment to federal income tax withholding in Box 2 of the W-2).
Any chance you are mistaken about the maxxing out Social Security and have it reversed? I could maybe see if they THOUGHT you were maxxing it out (and therefore they did not reimburse you for it), but then it turned out you are NOT maxxing it out (so they needed to pay Social Security so took it from your federal income tax withholding), it would make sense. But based on what you said, it seems like your employer messed something up.
It sounds like you may need to schedule an appointment with the payroll person at your job.
