When questioned at the beginning of the episode the butler stated that the chocolate room "somewhere near the living room" but in Shawn's flashback of the same statement the butler says "somewhere off the living room". This doesn't match with how Shawn's eidetic memory normally works and creates an unreliable narrator problem since his perfect memory is how he solves crimes.
When Sean and the others go into the kitchen to prove Jules's theory about two killers Rip's throat is moving when he is supposed to be dead in the freezer.
When Shawn noticed that Gus was missing in the mansion he worked out that he could be in a secret cubby hole in the room he was standing in. There was a chest of drawers next to a mounted moose head and after trying several variations of opening and closing drawers and touching the moose head a secret panel finally opened. It closed when Shawn entered. Once he found Gus he turned and immediately pressed down a bureau top to open the door. If he had never been in it before how did he know what to touch to open the secret door.
Billy Lips said he converted to Judaism in prison, yet he is eating Clizby's pork belly bites, which is not a kosher food. Jewish people are not allowed to eat anything made from pigs.
At roughly 37 minutes while Shawn is standing by the corpse of Rip in the freezer, speculating on his having killed Melinda Lane, you can see his (Rip's) chest rise and fall twice (breathing).
When Billy Lips (Steve Valentine) talks about performing Jewish rituals for the dead Highway Harry, Shawn rhetorically asks Gus "did he just do a mashup of Yiddish and Spanish?" However, the phrases Billy Lips said we're actually Hebrew words for said rituals, not Yiddish.
When Billy Lips (Steve Valentine) talks about performing Jewish rituals for the dead Highway Harry, Gus asks Shawn "did he just do a mashup of Yiddish and Spanish?" to which Shawn replies "He sure did." In reality, the words Billy Lips said we're actually Hebrew words for said rituals, not Yiddish.