Moving materials in a complex manufacturing environment is a difficult task. If you consider an average of 600-step process route requiring material movement between every step, managing those vehicles sometimes could be more difficult than managing the value added production itself. In contrast to machines, material handling vehicles are not fixed, they move around. Modeling them as another regular resource is not an option in this case.
Actually, it is not always the modeling or algorithm problem. Many times, it may be the infrastructure, which is beyond an Operations Research analyst's view. In many cases, it is hard to track vehicles or provide sufficient communication capabilities between machines, jobs and vehicles.
However, showing that an optimization based solution could make the overall system work better than the best solution that can be found within current infrastructure forces the hardware suppliers to design their equipments with better communication or tracking capabilities. This scenario is one of the many more examples existing in the real world, in which an OR expert can take proactive steps to change the environment to a better condition to work on. An optimization model is not always supposed to formed within the given constraints, it can also create its own constraint set.