In the innovative field of Physical Internet, the development of efficient Pi-cross-docking hubs (denoted Pi-hub) allowing quick, efficient and flexible transfer of containers will be a cornerstone. The paper addresses the control of such facilities. After a literature review in the field of the cross-docking control, a hybrid control architecture is proposed. The focus is held on the problem of containers routing in a perturbed environment. More specifically a reactive approach is presented. The simulation platform, protocol and results are then detailed.