If your concern is that you both used the same vehicle, it is ok to report the same vehicle if you are taking the standard mileage deduction and only reporting your portion. As long as the costs are not counted twice, it is allowable.
Since your income will be entered in separate TurboTax programs when filing Married Filing Separate, only enter your portion of the business miles. Your wife can use the same vehicle and only enter her portion of the business miles.
See Can I deduct mileage? for more details.
@etronguru
