If you download new content to an iOS device, or update apps, this content should be copied to your iTunes library when you sync the device. A number of people are reporting that iTunes 12.3 is no longer copying purchased content from their iOS devices. I am seeing the same thing on my iPhone and iPad, both running iOS 9.0.1.
This seems to be a bug, and I have filed a bug report with Apple. For now, I can’t find any workaround that will allow you to copy this content to an iTunes library.
Update: Apparently, this is the new behavior. Apple responded to someone who filed a bug report, saying:
This issue behaves as intended based on the following: Apps are no longer transferred from iOS 9 devices.
Apparently, this is related to App Thinning, a feature whereby iOS devices only download the resources they need to run apps on the specific device. To get the full app, you need to download it to iTunes.
This is a bit problematic. I have poor bandwidth, so I need to remember to no longer update apps on my devices, so I don’t have to download them four times.
However, I also tested this with music download from the iTunes Store, and it is not being copied either. So while the app sync issue may have a reason, the music sync does not.