I've had this happen to me several times as well. (Ability abruptly stopping after activating it).
Far as I can remember it seemed to happen if
1. I told UC to attack the targeted squad after activating ability (not sure if intentional to cause this to stop ability)
2. Facing of the UC or distance to target - if you try to use the ability if the the UC is facing away or too far away then cooldown will trigger but ability won't.
My PC is currently in for repair but I'll try to reproduce it when I get it back if nobody else has before that.
