Tax question??

If the payroll dept entered the time so that it wasn't treated as a 3 week check but as a 1 or 2 week check, then it would seem to appear that you are in a higher tax bracket, and more federal withholding would have been taken out. Social security and medicare would not change they would be 6.2% and 1.45% of your gross paycheck, respectively, and I'm not aware of any state that has tax brackets like the federal does. Your manager was correct that you might be able to get that back in the end of the year. But that will depend on whether you end up owing taxes or getting a refund.