The OpenGL window and the SceneExplorer window are shared among plugins to save system resources. This means that you will have to keep an eye on what plugin is using the scene right now and what you are actually modifying in these windows.
Most plugins will deliver their own UI elements to modify the scene so the SceneExplorer is more of a global tool. The simple SceneComposer however heavily relies on its functions as other plugins might too in the future.