The genetically perfect pig's collar changes from red to black between when Brian and Stewie leave the fair and when Brian and Stewie get to Stewie's room.
In the universe where everyone has two heads, the Griffin house has a picture on the wall of Chris with only one head.
Brian's dog tag briefly disappears in the fire hydrant universe.
Before human Brian jumps into the portal, dog Stewie was nowhere to be seen, but appears when human Brian jumps into the portal
In the universe where everyone has two heads, we first see a yellow house behind Stewie and Brian and then Cleveland's pink house- then back to the yellow house and back to Cleveland's pink house once again.