Since the controller changes, there's been some bugs, a few of them major, so here's the ones I've seen when using an Xbox One controller.
Changing keybinds for a controller does not save and will remain Default
WORKAROUND: Navigating the keybind menu with a controller will save any changes
Missing "Blank" option when assigning commands
This was very useful before when using third party software to allow more commands to be used on one button