This paper presents a deadlock prevention policy to obtain behaviorally optimal supervisors for flexible manufacturing systems with uncontrollable and unobservable transitions. The conditions of uncontrollability and unobservability of transitions are revealed in the sense of the implementation of a Petri net supervisor. Then, integer linear programming problems are designed to obtain a Petri net supervisor such that all legal markings are reachable and the number of control places is compressed. We also show that a controllable transition can be unobservable and self-loops can be used to disable the transition but do not observe its firing. Finally, examples are provided to illustrate the proposed approach.