They shouldn't be withholding on you unless the IRS asked them to, perhaps because you gave them a bad SSN in a prior year. Since this is a new job, there's no way the IRS asked them to do backup withholding, and you shouldn't count on ever seeing it credited to your tax return.
My guess is they do this for their regular wage employees to cover employment tax, unemployment tax, workers comp, etc. Since you're covering these yourself (at least in risk), you should not have a deduction. They should put you on W-2 so you actually get the benefit, or stop the deduction.