I am facing problem with iOS 9.1 when my app is installed for the first time user is prompted for location service permission, but alert view gets hidden instantly as soon as it is shown. Therefore app do not detect a user's location. Although allowing app to access location from setting.app works fine. It was working fine with iOS 9.0.2
The root cause for issue may be presenting a view or viewcontroller over popup. Try to call location service permission after 1-2 second delay there may be some issue of animation that is hidding alert view.
Problem may be happening if you are asking for location service permission from appdelegate or when application is just launched else it will work fine.