When Sophie stands up after being "shot" the little amount of blood on her blouse is in a rather roundish shape on her shoulder, however as the angles change the pattern varies several times to being splattered from her shoulder to the buttons.
There's no way to properly test the Morality Engine or prove the theory behind it, for humans.
As Milgram's Shock experiment showed (repeatedly) people will comply with an authority figure up to and including torturing an innocent subject to death. Other psychologists such as Jung showed that humans follow the herd, their morality is dependent on the group and perceived expectations. They will never give honest answers to the baseline questions, but instead give the answers they believe are desired by the tester or society. Without the baseline there's no way to prove the efficacy of the treatment.
Everybody refers to the chimpanzee as a monkey, chimpanzees are apes. (Monkeys have tails, apes do not) As biologists Miller and Stutzer would certainly know the difference.
When Jane and Lisbon are talking to Professor Stutzer, actor John Aylward flubs his line when he says to Jane, "You are a skeptical." This line doesn't make sense. He presumably was supposed to say, ""You are a skeptic", or maybe "You are a skeptical [person]." Had this been a movie they would have re-shot it to get it right, but on TV they don't bother, as even something as simple of this little flub takes too much time, and therefore money.