If you look at Prism 2.0 (Composite WPF), you will see the old codes have been commented out
// We register the container with an ExternallyControlledLifetimeManager to avoid // recursive calls if Container.Dispose() is called. // Container.RegisterInstance<IUnityContainer>(Container);
Base on this post http://compositewpf.codeplex.com/Thread/View.aspx?ThreadId=52999, that is because the container’s already registered itself.