After upgrading to iOS 9, I can't transfer purchases from my iPhone to iTunes. It happens to just start the process, then it finishes without transferring anything. However, I can still transfer purchases from my iPad with iOS 8.4 like before.

iPhone 5c, iOS 9

iTunes 12.3

MacBook Pro 13" with Retina Display Mid 2014, OS X El Capitan

Apparently, not many people happen to use this "transfer purchases" feature so it didn't get any real attention. I used it a lot, I used to update my apps on my iPhone, transfer them to iTunes and updated my iPad apps using iTunes. Still, I can update my apps using iTunes and update apps on all my devices.