Sorry for the lengthy post. Please bear with me!
After upgrading my Moto G2 to Marshmallow, I faced the same issue as a lot of other users with the contacts storage. They had disappeared and yet showed up on WatsApp. I fixed that issue after deleting all contacts, clearing the cache partition and then syncing with my Google contacts.
However, the default Google contacts doesn't allow me to view, add or delete any contacts. Using another app helped view the contacts but I still can't add a new contact. I have to add on Google contacts and then sync.
The error message says "You have disabled a required permission". The Contacts Storage's permission section is disabled. So I haven't changed or can't change any permissions. The other sections such as storage are accessible.
What is the resolution? Is factory reset the only solution?