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.
Apparently As NetherLinks explained in the comments, not many people happen to use this "transfer purchases" feature so it didn't get any real attention it's because of the App Thinning feature Apple introduced in iOS 9. I used it Basically, a lot different version of each app is downloaded on any device. So, I used to update my apps downloaded on my an iPhone, transfer them to iTunes and updated my cannot be used on an iPad apps using iTunes. I guess Apple is aggressively moving towards cloud-based features (iCloud as the hub of computing), so they are disabling the features that delayed this process See image below taken from App Thinning page in iOS Developer Library.

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.
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. I guess Apple is aggressively moving towards cloud-based features (iCloud as the hub of computing), so they are disabling the features that delayed this process.
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 any 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.
