After Brennan suggests that they run the simulation without the rubber-soled boots, she and Sweets argue after Sweets states that Neil would not have put on his boots after shooting himself up with heroin. Brennan's suggestion would account for this fact, and therefore, the argument is unnecessary. It would make more sense if Brennan's suggestion regarding the simulation came after the argument.
(at around 14 mins) Booth, Brennan, and Sweets are examining a painting made by mental health patient Neviah Larkin. Brennan notes that in the painting Neviah "... replaced Longinus, the soldier who drove his spear through Christ's side, with her own face. Further, "she's put the murder victim's face in place of the crucified devil." In keeping with the biblical theme, the crucified victim in the painting, whose face was replaced, would be Jesus - not "the devil."