When creating a keyboard shortcut through the keyboard settings and another shortcut already has this key combination it lets you choose which to keep. If you choose the new one there are now 2 shortcuts that are using that combination and if you try to remove either it just removes the new one or will not allow you to remove either. If you close and start up the settings manager again it only shows the new one (if you don't try to remove either) which is why i put this as fairly low priority.
Fixed in git master branch with commit 849aa7824f8a482496c05b1fd77099e062d1c92b.