Thin films often present domain structures whose detailed evolution is a subject of debate. We analyze the evolution of copper films, which contain both rotational and stacking domains, on ruthenium. Real-time observation by low-energy electron microscopy shows that the stacking domains evolve in a seemingly complex way. Not only do the stacking boundaries move in preferred directions, but their motion is extremely uneven and they become stuck when they reach rotational boundaries. We show that this behavior occurs because the stacking-boundary motion is impeded by threading dislocations. This study underscores how the coarse-scale evolution of thin films can be controlled by defects.