Can't transfer purchases from iPhone to iTunes in iOS 9 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.
Actually, this is not a problem.
Transferring purchases from devices with iOS 9 has been disabled by Apple. This is the response they gave to submitted bug reports regarding this issue:


  Apple Developer Relations 18-Sep-2015 02:51 PM
  
  This issue behaves as intended based on the following: Apps are no
  longer transferred from iOS 9 devices. We are now closing this bug
  report. If you have questions about the resolution, or if this is
  still a critical issue for you, then please update your bug report
  with that information.


As NetherLinks explained in the comments, it's because of the App Thinning feature Apple introduced in iOS 9. Basically, a different version of each app is downloaded on each device. So, apps downloaded on an iPhone cannot be used on an iPad. See image below taken from App Thinning page in iOS Developer Library.