Best Answer - Chosen by Voters
You need to contact the Department of Labor in the nearest city. This is illegal, and the dept of Labor was established to stop this sort of abuse by employers. Even if there was a miscalculation on their part, they are required to show you proof before there are any deductions made on your paycheck.
Take all of the documentation that you have, all of your check stubs, time sheets, any sort of letters that you have written, including your two weeks notice, to the Labor Department and they will assist you. They will contact the employer and they will have to show proof. Since their "miscalculation" occurred so long ago, I will bet that they will have a hard time coming up with proof. Since you have not seen any proof, and were not notified immediately upon the discovery of the miscalculation, then they cannot withhold pay from you.
Even if you are not 100% sure that they shorted you, you should still notify the dept of labor that they are not following payroll laws.
If the miscalculation was a real thing, then you may need to contact the IRS, as you have paid too much in taxes. The IRS will penalize the employers for not following tax laws.
Did they do the same thing to all of their employees? Or was it just you?