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.
During the preliminary examination of the remains in the church and later during the autopsy, Bones consistently says that the horns are made of 'real bone'. The horns are dermal growths (like nails, claws and hooves) and thus are made of keratin. Some animals have indeed the bony protrusion inside the keratinous sheath, but the victim's horns were implants, so they obviously lacked the bone component. No one with any background in medicine or biology would call horn a 'bone'.
(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." Except that in the painting, it was the devil hanging on the cross, not Jesus. She was depicting herself as the angel killing the murder victim as the devil.
The victim is said the have fallen into a transformer. In fact the equipment he fell onto is a fused disconnect switch.
Half way through Booth searches a nurses car and finds bags of pills. Booth holds up a bag that appears to hold pills and says that he found heroin. Heroin is stored in powder form. However, a closer look at the bag shows it filled with small, glass, powder-filled vials with black caps, looking very much like pills at first glance.
When Booth and Brennan are searching the nurse practitioner's vehicle, Booth touches the evidence with bare hands. This would definitely compromise evidence.