After you file

@GiseleD  

The employer was a small business military contractor. The payroll office was just a few people. What it looks like to me is that this was intentional. I could provide you a snap shot of the pay stub through private message for you to see exactly what I am talking about.  I have looked this up and I have found no information on an employer taking money out of your federal or state tax withholdings. It was my understanding that they had to put it into a separate account as to not be able to make interest off of it. What it looks like is they were somehow able to just say that subtract money that was already supposed to be withheld and in my final paycheck not even withhold tax for federal or state.