Hi Jake,
As with the service department, you don't want to create any barriers between your department and the body shop. Working together toward a common goal is a lot more productive and far less aggrivating than working against one another. Before charging your body shop a restocking fee sit down with the body shop manager and discuss the situation. Try to find out why they are returning so many parts. Working together, perhaps you can eliminate or drastically reduce the problem. A solution worked out this way will go a lot farther and have a lot more value than what is gained by charging the restocking fee.
Of course, the aforementioned method is only possible if the manager of the other department can be reasoned with. If he or she cannot be, then a restocking fee might be in order. If you do decide to charge one make sure its consistent with company policy and with similar action taken toward other departments. Also, you might explain to the body shop manager that you are charging it only to offset the additional expense incurred from the returns.