Continuity mistake: In the scene with the multiple versions of Stewie and Brian come back to 1999, one Peter is with one of them. When Stewie asks everyone to vote between 9/11, Peter is standing in the foreground, but disappears when one of the Stewies says Brian had his throat slit.
Continuity mistake: When Stewie is playing golf at the top of the stairs before attacking Brian, the layout of the upstairs floor changes quite radically between shots. First Stewie is playing golf with the stairway behind him. Then when Brian puts on the disguise and walks past, there's suddenly a wall behind Stewie. Brian walks off to the left and Stewie begins to chase him that way, but in the next shot Stewie is chasing Brian off to the right. In that same shot you can see that Stewie is running away from the stairs, but in the next shot, without changing direction, he pushes Brian down the stairs, which mysteriously have appeared in front of him.
Continuity mistake: During the scene where the Griffins have Tom Brady over for dinner, when we first see the establishing shot of everyone at the table, Chris is sitting with an empty chair between him and Tom. However, when he asks if he can call him Tom along with Lois and Meg, he is sitting right next to Tom, with no empty chair between the two.
Continuity mistake: While Meg is at the kitchen table telling the family about her new life with God, you will notice that Brian is sitting to the right of her. As she starts to ask that everyone hold hands, take notice that Brian is not in that chair and that Brian's plate and utensils are moved closer to Meg. As the shot pans out, Brian is back in that chair.