There have been reports on the 2.1 PTR that some Nephalem Rifts do not have enough mobs to kill in order to complete the rift. Yesterday I had a three-level rift that I cleared and swept through again to double check there was nothing left to kill and yet I had only reach 79% completion. It happened again later that night but I was in the 90% area then.
Blizzard are thankfully aware that this is an issue, however it can’t simply be hotfixed but will have to wait for a larger patch. Here’s the skinny from
I haven’t seen such reports for Greater Rifts.