iOS 9 updated apps won't copy to iTunes
After updating an iPhone 6 to iOS 9.0, when doing an automatic sync or manual backup to iTunes 12.3.0.44, any apps that have been updated on the iPhone do not get copied (backed up) to iTunes anymore. If the app has been updated on iTunes but not the iPhone, then iTunes will correctly update the iPhone -- just not the other way around.
Similarly, using iTunes File -> Devices -> Transfer Purchases no longer works with any device that's been updated to iOS 9.0.