I ran into this when deploying an event receiver that would update the master page of all sites (SPWeb objects) when activated in a particular site collection (SPSite object).
Accessing referenced file from is not allowed because the reference is outside of the App Web.
The problem is described and resolved here: http://mctalex.blogspot.com.au/2013/07/powershell-fix-for-app-master-problem.html.
I adapted this script to something a bit more readily reusable: https://github.com/skaggej/powershell/blob/master/Set-SPAppWebMasterPages.ps1. Just enter the root URL of a site collection and it will update the master pages for all app webs within it.