Whenever Brian and Stewie went to another Universe there was always two versions of them, but when they went to the Disney universe, there was only one version of themselves.
Stewie's prediction about Brian's reaction to seeing Lois in the first alternate universe is changed in the Adult Swim version. On Fox Stewie's line is "put your penis in a wheelchair", on Adult Swim it was altered to "Your penis would shoot right off"
In the fire hydrant universe, Brian's dog tag briefly disappears.
In the Two-Headed Universe, 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.
The Sistine Chapel should not exist in a universe without religion.
Here are the universes Brian and Stewie visit:
* A futuristic universe where Christianity never existed and the Earth became more advanced.
* A universe based on The Flintstones.
* A universe where the USA never dropped the Atomic Bomb on Hiroshima, Japan meaning that the Japanese never surrendered.
* A universe where everyone has two heads: a happy head and a sad head.
* A universe that is mostly ice.
* A universe where everyone has to take a poop just now.
* A universe where everything is drawn by Disney.
* A universe based on Robot Chicken.
* A universe where Frank Sinatra wasn't born to influence John F. Kennedy's election, Richard M. Nixon won the election and botched up the Cuban Missile Crisis plunging the Earth into World War III, and Mayor McCheese was assassinated by Lee Harvey Oswald.
* A universe where everything is blocky and crudely-drawn.
* A universe that is mostly fire hydrants.
* A universe that consists of homosexuals.
* A universe that is live-action (Brian is depicted as a Labrador Retriever).
* A universe where everything is animated like a Washington Post political cartoon.
* A universe where it's only inhabitant is a far away guy that yells compliments.
* A universe of misleading portraitures.
* A universe where humans and dogs have switched roles.
When Stewie and Brian go to the universe where everyone has two heads you can see a portrait of Chris with just one head.
When the cast of How I Met Your Mother appears before King Stewart, they perform a short scene referencing the Bro Code. However, the section of the Bro Code they mention has nothing to do with the scene (a full-length book version of the Bro Code had been published about 7 months before this episode aired). Barney cites Article 15-b and describes it as "the heart of the Bro Code"; this sub-article doesn't exist, however, as Article 15 is "A bro never dances with his hands above his head."
The closest article relating to what they're talking about in the scene would be Article 101: "If a Bro asks another Bro to keep a secret, he shall take that secret to his grave. This is what makes them Bros, not chicks"
During the talent show scene, Seamus is wearing a cut-open shirt and is shown to have a human body, however in the episode Ocean's Three and a half when Seamus is at the spa with Peter and his friends, his whole body is shown to be wooden with the exception of his head.
Chris does not appear in this episode.
Roy Scheider's final TV appearance before his death.
In this episode Stewie said he was shopping for hats. However, he said that he's not a hat person in When You Wish Upon A Weinstein.
Jillian's last name is revealed as Russell.
An orange peel, a picture of Lois eating a turkey leg, and the cut-off crusts of Chris' peanut butter and jam sandwich. (Whoever packed Meg's lunch either forgot about her peanut allergy or was actively trying to kill her.)
This episode reveals that Kevin Swanson, Joe's son, died in Iraq, explaining his sudden disappearance from the show (also, in the DVD commentary for Peter's Two Dads, the creator Seth MacFarlane said that he was a very boring character). However, this is later retconned in Season 10 by stating that Kevin was MIA (Missing in Action).
When Peter, Joe, and Cleveland arrive at Quagmire's house, there is no wheelchair ramp on Quagmire's front step, yet somehow Joe manages to get into the house without any difficulty.
The Adult Swim version replaces the William Shatner joke at the beginning with a new brief shot of people on the convention floor.
The song Brian growls while chewing a cross is "The Right Stuff" by New Kids On The Block.
When Rush Limbaugh comes out of Michael Moore's house, he is putting on his jacket, but the video Lois shows has him coming out of the house with the jacket already on.
During Brian's "interview" with Stewie, he asks Stewie what it was like performing the words of Oscar winner Diablo Cody. But Diablo Cody didn't win her Oscar until February 24, 2008 - 11 months after this story was set.