In the advanced technology universe, Stewie tells Brian that there is no religion. He then takes Brian to the Sistine Chaple. If there is no religion, there wouldn't be any chapels.
When Stewie and Brian are in the Doubleheads Universe, before leaving it, they are standing in the front with the door open. You can clearly see a picture of Chris in the back wall with just one head, when he should have two.
During the Disney Universe "Its a wonderful day for pie" musical number, the front door is opened by Stewie and Brian. It stays open up to when Cleveland (drawn like Bambi's Flower) walks in, but then is closed and open by Chris. It can be seen open wide open, but is closed when Herbert (drawn like the queen's old lady disguise from Snow white) offering a red apple.
After Mort walks in, the cast yells "Jew!" and meg (drawn like the little mermaid's Ursula) grabs him with her tentacles. The door is missing.
In the Disney universe, the pads on the bottom of Brian's soles continue to change design and disappear between shots.
Stewie and Brian's animation style changes to match the Disney universe and a couple other universes, but does not change for yet others, such as the low-resolution universe.
Stewie says he'll blow Brian's mind like the steropticon did in 1910, misnaming the stereoscope for the stereopticon.
In the first universe they visit, chapels seem to exist despite the lack of Christianity.
When Mayor Adam West stands on the scale at the fair, it reads 15 pounds. He says he's 95% helium which would make him 300 pounds normally.
In the Two-Headed Universes, while most characters Happy Head was on the right and the Sad Head was on the left, Stewie's heads were the other way around.