We got a 1099 misc. are employer said it was for mileage. On are check stub is shows mileage taxable and mileage reimb. We paid tax on mileage taxble but not on mileage reimb.
Are employer said that the 1099 was for mileage reimb. I thought that 50 percent was tax free and the other 50 was taxable. Why are we having to pay taxes on 100%.

No, mileage reimbursement is generally taxable, but then you offset it by claiming your mileage as an employee business expense. Unfortunately, if you have a LOT of mileage, you will run afoul with the Alternative Minimum Tax.

If you present a precise mileage log and get reimbursed at or below the GSA mileage reimbursement rate, then the employer CAN treat it as a non-taxable reimbursement of expenses.