The Night of the Bubbling Death - S3-E1
Revealing mistake: As West drags the body of a bad guy out of the scene, the supposedly unconscious man is holding his head up so as not to have his head dragged through the dirt. A truly unconscious person's head would flop back on to the ground.
Revealing mistake: On 10/9/06, John entered the storage facility and reached towards the light cord. He formed a fist, as if grasping the cord, but his hand was actually several inches from it. It was clear that he was not actually holding the cord at all, but then he pulled his fist down and the lights went on.