Not really. My employer lists reimbursements on my pay stubs each month (probably for record keeping) but they are not included in box 1 wages on my W-2. Do you actually have your W-2 yet? It's too early for most businesses. You may be confusing yourself by trying to use a pay stub.
If the reimbursements were added to box 1 wages on your official W-2 then you will be able to deduct your expenses. Were they also added to box 3 and box 5?
As a separate but related issue, reimbursements are only non-taxable with an "accountable" plan, where you submit mileage records and other receipts and you only get reimbursed for expenses that you prove with records and receipts. If you don't submit records, or your employer pays a per diem and doesn't require proof, then that is a non-accountable plan and it must be taxed. Then you deduct your expenses against that taxable income.
I assumed from other things you said that you have an accountable plan--if your employer is adding reimbursements to your box 1 W-2 and you have an acceptable plan, he's doing it wrong, or at least unnecessarily. But you can deduct expenses against taxable reimbursement, just not against non-taxed reimbursement.
Do you have your W-2 yet?
