You download the (from iPhone) missing apps directly with your computer iTunes under Purchased
iOS 9 app thinning do not allow apps from iPhone to be a master copy on computer iTunes.
App thinning: Only the resources your device(s) needs will sync over saving space.
Before iOS 9, if you have an app that is compatible (universal) to iPhone & iPad, all the app resources are sync over.
Now, iPhone get the iPhone resources not those for iPad and vice versa.