All of those suggestions to re-download apps from the purchased list are not solving the issue but rather putting a band-aid on it. Previously, if you downloaded a new app on your iPhone / iPad or updated an app on your iPhone / iPad, if you plugged that iPhone / iPad into the computer and clicked sync, the new apps, and updated apps would transfer through to iTunes. This no longer happens, requiring users to manually download new apps, and update existing apps twice, once on their iPhone / iPad and once in iTunes. This as some have mentioned is an issue if you do not have unlimited home broadband, and it is also a waste of time to download and update apps twice. For me, this issue has been ongoing since iOS 8.3, on my iPhone 6, and iTunes version 12.1.2.27
I found a comment to an article online a while ago, but unfortunately do not remember where I read it, that said that this is due to the app thinning feature of iOS 9 where apps only download incremental updates or the pieces of code/files they need. For example, an iPhone SE does not need the same graphics files, with the same resolution, as an iPad Pro 12.9 would. Therefore, each iPhone / iPad downloads a "different" portion of each app while iTunes downloads the entire app, and as a result, any apps downloaded or updated on an iPhone / iPad cannot transfer over to the computer because it is not the exact same app.
I really hope Apple will fix this, and I really hope someone from Apple is reading this forum.
I am on the iTunes version 12.5.1.21; iOS version 10.0.2; and iPhone 7 Plus