Metaphor and Numb3rs in 'Conspiracy Theory'

I am currently watching a recorded episode from TNT that I missed, 'Conspiracy Theory'. At about the halfway point Charlie explains "Simpson's Paradox" (although he doesn't explain the paradox very well), and gives some baseball statistic to back it up, and then this whole exercise is supposed to imply that "You go with what you know, not what you don't". I am completely lost. The numbers don't seem to add up, and the logical leap to the moral of the exercise is a mystery to me. Huh? If any kind souls have this episode on DVD and can explain it to me I would be very appreciative. My husband with a math degree is also lost, and upset that the numbers seem wrong, giving him more reason not to watch with me :(