This is just false. The entire premise of this thread is false. I wonder how much experience you have on other Stern games besides X-Men. If something is flashing - it MEANS something...just like any WMS game. I turn on Monster Bash - every shot is flashing...and it makes sense. I know I have to shoot the Wolfman 4 times, the Drac targets, Frank, etc.
Sterns games are generally designed and programmed by the same people who made the WMS games. For better or worse, they're generally similar experiences.
In the case of X-Men, the game clearly has software issues, but if you can't figure out what to do - that's on you (and your son lol). Shoot lit character shots, start their modes. Shoot the big green LOCK inserts, lock the ball for Magneto Multiball. Shoot the scoop when Villain is lit...hmmm, what could that do - oh, I dunno, start a VILLAIN MODE!??!! Wolverine's Multiball - some shots are lit, shoot them and he turns a corner and confronts a guard - then, only Wolverine is lit, so - shoot him, kill the guard (Jackpot).