You're still not providing enough information. Let me try some examples.
Let's say you have $30,000 in salary and commissions for the whole year with no chargebacks. Your W-2 would show $30,000 in box 1 (wages), box 3 (social security wages) and box 5 (medicare wages). Your box 2 withholding is whatever federal tax was withheld, your box 4 social security tax will be $1860 (6.2% of box 3) and your medicare tax will be $435 (1.45% of box 5).
(On your actual W-2, boxes 3 and 5 may be different from box 1 depending on whether you participate in a 401k or certain other benefits, don't worry about it for now.)
Now, let's say you have the same gross wages, but you had $5000 in chargebacks for canceled contracts. You need to know, will your box 1 wages still show $30,000? Or will it be adjusted to $25,000? Will box 3 and 5 be adjusted as well? Is box 4 still 6.2% of box 3, and is box 6 still 1.45% of box 5?
Generally speaking, if the chargebacks are in the same year as the wage payments, the employer should adjust box 1 of the W-2. In that case you won't be double-taxed on your income tax, you will only pay tax on the net amount you earned. If they don't adjust box 1, there is a procedure to claim a tax deduction, but it depends on the amount of the chargeback. And I would also complain to the state labor board in your state that they are reporting your income wrong and causing you tax harm.
I'm not sure if boxes 3 and 5 should also be adjusted, that's more complicated and I would have to do some research.
But I really can't tell you if things are right or wrong until you look at your actual W-2 and compare it with your pay and chargebacks to see if boxes 1, 3, and 5 have been adjusted for the chargebacks or not.
