I would recommend discussing this with your employer. 

If there are employee business expense reimbursements for employee business expenses that need to be included in income, those amounts need to be reported through the W-2 not on an additional 1099-MISC. Ideally, your employer should set up an accountable plan for reimbursed expenses (if they did this they could just reimburse you, and you would report nothing on your return).

They should amend your W-2 and there payroll forms to include the reimbursements as taxable income on your W-2. You should extend your return to give them time to do this. If they refuse, you could follow these instructions from the IRS to report an incorrect W-2.

Ask your employer to create an accountable reimbursement plan. 

See the following: 

If your employer has a policy that covers reimbursements or allowances for mileage, you need to determine whether the policy is an accountable plan before claiming any deduction. Assuming that all mileage covered under the policy solely relates to your employer’s business, the IRS treats the policy as an accountable plan if you must account to your employer for your business automobile expenses and return any excess reimbursement within a reasonable period of time.

If these conditions are met, your employer doesn’t have to report the reimbursements as taxable wages on your W-2, which means you don’t pay income tax on them. But, since you receive tax-free mileage reimbursements, it means you’re precluded from also taking a deduction for the same mileage expenses. However, if your reimbursement or allowance doesn’t cover the entire expense, you can deduct the unreimbursed portion as if no reimbursement policy exists. Your Form 2106 will show your expenses and the amount of employer reimbursement; the difference between the two will be your deduction.