Have you tried going to preferences and checking 'apps' under where it says 'automatic downloads'?
For Mac it's located under itunes>preferences>store tab.
I believe checking this option should automatically download any purchases made from your ios device, to your itunes. (I just discovered this option after searching online so I haven't tested it yet, and can't at the moment.) I think I remember this option being there before, but I thought it was a precaution... to download the purchased app immediately, just in case your device is lost before you get a chance to sync. Now I guess it's the only way to automatically transfer (or download) new apps from your ios device to your itunes. ??
Along that note, there is the 'music' check box next to 'apps'. Does that mean you have to check 'music' as well if you want music purchases from your ios device to sync back to itunes? I thought for sure, music purchases on an ios device would transfer back to itunes during the regular itunes/ios sync.
Anyway this is really weird, because I'm almost positive apps used to sync along with music and everything else during normal sync (including app updates). I guess for some reason Apple decided to change this?
This is all very confusing, Apple. Whatever happened to "It just works"??