So mysteries have this thing called "prompt" (it is listed when you read the skill). Prompt skills make sure the skill happens during the turn regardless of where the ninja is located and does not override a standard. So if you have a ninja on po4, then it will go off if there are no restrictions on the ninja.

Non-Prompt skills needed to be used before the ninja's standard go off. This means for Pain Tendo, you have to use the skill before the ninja before him finishes their standard attack. Otherwise, the mystery will go off next turn. Players that are aware of it would train themselves to launch the skill right after the opponent's ninja finish their move to avoid the skill being interrupted.

Not sure why you did not figure this out when you have been playing for nearly two years unless you quit during your learning phase.