最後に追加されたビューボタンのみがクリック可能であるようです。
self.splitViewController = [[[ViewController alloc] init] autorelease];
self.splitViewController.delegate = self;
ViewController *mainViewController = [[ViewController alloc] init];
ViewController *detailedViewController = [[ViewController alloc] init];
UINavigationController *mainViewNavigationController = [[UINavigationController alloc] init];
mainViewNavigationController.navigationBarHidden = YES;
UINavigationController *detailedViewNavigationController = [[UINavigationController alloc] init];
detailedViewNavigationController.navigationBarHidden = YES;
[mainViewNavigationController pushViewController:mainViewController animated:YES];
[self.splitViewController.view addSubview:mainViewNavigationController.view];
[detailedViewNavigationController pushViewController:detailedViewController animated:YES];
[self.splitViewController.view addSubview:detailedViewNavigationController.view];