I have noticed this problem intermittently throughout the beta, but sometimes command stops working properly. I think I have figured out how and why, and have a save.

If you have an army with a sovereign and a champion in it, and the sovereign doesn't have the highest initiative, then command doesn't work properly. I've seen it have no effect at times, and then at other times instead of giving the unit an extra immediate move, it gets a double move on its turn. 

Load my save and attack the wolves and it shouldn't work properly. Reload, and change the equipment where Relias has higher initiative and it should work properly.

https://dl.dropboxusercontent.com/u/77858773/scenario1.EleSav