When Brian originally performed The Peanut Butter Jelly Time in "The Courtship of Stewie's Father", it was daytime, and the doorknob is missing. When Stewie performs it, it's nighttime, the doorknob is restored, the bottom of the couch looks different, the boarder of the door is brown but in the newer one the boarder of the door is blue and the sofa is further away from the door. When Brian tells Peter "Aw, don't feel bad, Peter. Hey, I know what'll cheer you up," Peter is supposed to say "I don't think I'm in the mood."
When Bertram enters Stewie's room, you can see Stewie sleeping in his bed. As the shot changes, Stewie is missing, then reappears.
After Bertram shoots Leonardo da Vinci, his crossbow appears reloaded when is it grabbed by Stewie.
During the fight with Bertram, the blood on Stewie's mouth disappears, but later reappears.