In Visions of Enmity, sometimes GR keystones (from Rift Guardians and The Final Cache) are missing, eg. after killing 3 RGs only one keystone drops, or there are no keystones in the cache.
This could be caused by “pets collect stuff”, because when I dismissed my pet, all RGs dropped keystones as usual.
I’ve noticed this too.
I can run 6 Visions, regardless how many Levels each has, and end up with 200 or more Greater Rift Keystones.
A couple of days ago I finally reached Torment XVI (T16) and started farming and upgrading my Legendary Gems. I had 23 GR Keys to start with.
After running several Greater Rifts I was down to 2 GR Keys. So, I decided to run some Visions to gather more. By the way, my Follower has Cain’s Destiny equipped. I completed 6 Visions. I checked my total Greater Rift Keystone stash and only had 6.
That means, in this PTR, after completing 6 Visions (some Levels with Guardians), I only picked up 4 GR Keys. 
This is when I decided to go back and run Nephalem Rifts instead. At least they give me 3 to 8 Keys for each Rift I run. 