There is an issue with Cornerstone that has been there for quite a long time, but I have worked around it and haven’t had a chance to inform you about it. I would like to see this fixed at some point, though.
The issue is on the Edit Menus page in the admin area. When you go to edit a menu item, any extra fields added by other plugins get duplicated. So, for example, I am using a permissions plugin that allows me to show or hide the menu items based on roles. But the fields/options show up before AND after the Cornerstone fields. I disable the Cornerstone plugin, and the permission fields show up only once with no issues (see screenshots of Cornerstone activated and deactivated). I reactivate Cornerstone, and they get duplicated again. The issue is that every time I make changes to the menu, I have to make sure that the top fields and the duplicated/bottom fields match or they will not work and I get errors. So there is something in the Cornerstone code that is causing a duplication.