Changes and Known Issues in iOS 9

Enterprise Developers and In-House Applications

In iOS 9.0 and later, Apple has changed the way in-house apps are authorized on devices.

Previously, an app distributed with an in-house signature and mobile provisioning profile could be installed and launched directly. At the first launch, an "Untrusted Enterprise Developer" warning would be shown, and the app developer would need to be "trusted" through the device's Settings.

See the "Untrusted Enterprise Developer popup" on Can't install an app on a device? Things to check for the detailed steps.

Development Apps Cannot Overwrite App Store Apps

In iOS 9.x, Apple has changed the way development/in-house apps and App Store apps are installed.

Previously, a development app with the same bundle identifier could overwrite an existing App Store app. This could be dangerous, as a legitimate App Store app could be replaced by an unknown app.

Now, when trying to install a development app with the same bundle identifier as an app already installed from the App Store, the installation will not proceed.

See the "iOS install popup did not appear" on Can't install an app on a device? Things to check more information.