Syncing updated apps from iTunes to iPhone

iPhone 6 plus running iOS 8.3

iTunes version 12.1.2.27

Macbook Pro (Late 2011) OS X Yosemite 10.10.3

I am having trouble syncing updated apps from iTunes to iPhone, 2x apps are recommending to update via iTunes rather than iPhone, more a software issue with said apps rather than a size issue as far as i can tell.

I have been trying to do this for days, searched the community and followed advice, I.E. turning auto updates on, still have no joy 👿 normally i just update my apps through the iPhone. i have also noticed that some of my music hasn't been transferred to iPhone (noticed the little cloud download symbol next to some songs).

To be honest i think I've always had trouble syncing be it music, photos, artwork, apps, hence the reason i update through my iPhone. This issue is starting to really annoy me as i have paid Apple a fair chunk of hard earned cash over the years.