You need to bare in mind that AI system will always target the target in front of you unless stated otherwise on the ninja tooltip. Such as Kakashi who targets the lowest HP in any given team, there are many other ninjas with similar skills. Like your ninjas up in a way that makes them more effective against the opponent you want to beat. Some mystery skills will also only trigger if certain conditions apply like Kakashi beheading blade, who will only attempt to execute a ninja with health below a certain percentage.