Those are hardly plot holes. The first one, Scott isn't a psycopathic monster, he just wants to find devoted fathers. And the second one could just be a coverup. Criminals getting killed without a trial leads to negative public opinion.
Try these:
1) How does Madison know Scott? Why does she recoil in shock upon hearing his name?
2) Why do Scott's thoughts never suggest that he is the Origami Killer, and indeed, prove the contrary?
3) What exactly does Ethan DO during his daily blackout?
As for Scott...do you really think he would kill you? The ONE MAN willing to risk everything, endanger himself, to kill, even to DIE for his son, and you think Scott would shoot him?







