Recently working with a customer on an issue and since we found the solution, I want to post it here since it took us a bit of digging to find:
From the server we were unable to manage the User Profile Connections ie Could not add a filter
We looked at permissions, problems with sync service, and a bunch of other things.
As it turned out the solution was simple, while I was digging thru ULS logs trying to find the permission issue it was an IE issue. By adding the URL to the Compatibility View Settings (Go to IE -> Settings -> Compatibility View Settings) we fixed the issue.
This was the site where I originally found the solution https://sharepointthing.wordpress.com/2013/10/09/problem-with-sharepoint-2013-and-internet-explorer-11/