I am experiencing the same with my Mac iTunes (running latest for Mavericks OS version).
First I noticed that the "News" app disappeared from my phone; as an Apple app it's not deletable.
Then I noticed that the UI on the phone for the apple "Podcasts app was the 8.4 version - not the newer look.
So something was messed up -- it looked like I had a partial upgrade and I had lost at least one apple app.
With Apple support guidance I tried restores -- restore from back up using iTunes did not fix the problem; a fresh restore as a new phone worked for those problems but the text on the "Settings" menus were now alll misaligned and displayed improperly.
I then, with apple support guidance, did a hard reset from the phone and then a restore and the phone behavior cleared up -- but this problem with the Home Screens display loading forever remained.
Then that night after just a normal backup and sync, new problems - the Apple iTunes Store app and App Store apps both disappeared.
That along with an aggressive screen rotation issue seems to indicate there is or can be a corruption to the 9.x stuff.