The acceleration of masses m1 and m2 can differ due to the movement of the pulley they are attached to, which is influenced by mass m3. When one mass moves upward, its acceleration is augmented, while the downward-moving mass experiences a diminished acceleration. This difference arises from the dynamics of the pulley system, where the motion of the pulley affects the tension in the strings. Analyzing the system with free-body diagrams can clarify these relationships. Understanding these concepts is crucial for solving problems involving constrained pulley motion.