I can't find a definitive answer to this, but I can see a lot of people are having the same issue.
I have setup magento 2.1.0 and all is going well. However the cron job fails on the update script.
I have the following error:
[2016-08-26 08:21:02] update-cron.ERROR: Cron readiness check failure! Found non-writable paths: /home/<USER>/public_html/app/design/frontend/Magento  
Furthermore this file only exists under the pub/static folder and not under app/design/frontend. Its all very confusing.
I have run the permission changes from magento via ssh, I even tested this with cmod 777 but still to no avail. I have also tried running the cron job as both the user and root but still the same issue.
This is on a VPS running CPanel and WHM PHP version 5.6.24
Am I missing something stupid here or can anyone advise a way to fix this?