When Charlie Epps is writing a quadrillion on the whiteboard, the writing alternates between shots. Most noticably when he first writes it down, there is a significant downward tendency of the 000 groups. In the next shot, they are pretty much horizontal. Also the shapes of the commas alter.
Season 4 - Episode 4 "Thirteen"; The episode revolves around a man killing people with the same first names as the thirteen apostles (Mary Magdalene being the 13th), and killing them in a similar fashion in which the apostles died. At one point, Colby and David find a box with a mannequin's head in it. This is a reference to the film Se7en, in which seven people are killed for committing one of the seven deadly sins. The film ends with the main characters finding an actual head in a box.