In this movie Stewie can't swim but in previous episodes he could swim perfectly fine such as when he dived into a tank to kill a lobster.
When Brian and Stewie are in the bar trying to get Stewie drunk, after Horace sets Stewie's drink on the table, the olive in the glass mysteriously moves from the glass to the table.
In the pool scene, where Peter is trying to shake Stewie off his arm so as to throw him in the water, an opened book and a cocktail drink switch places on the ground, and finally disappear.
In the scene where Brian and Stewie are playing chess inside the Winnebago, the game board and pieces are completely unaffected by the heavy rocking of the vehicle shown in the overview shot opening the scene. On top of that, the rocking seems to have stopped completely once the scene cuts to the interior.
Tom Tucker's mustache is revealed to be fake when he is asked to turn it in along with other studio property. But in the retirement home scenes that ensue, he has it back and it has turned gray with the rest of his head hair, implying that it is real.
It is not possible to hear a naked man whimper in the vacuum of space.
When Stewie runs into Quagmire's room in the motel, Quagmire is tied to the bed and his hair style is different (the style it is when Peter meets him as a sailor in the TV show). This is mentioned on the commentary.
When Stewie steals Quagmire's Winnebago, "Eastbound and Down" is playing, but Stewie and Brian are heading West - to California.
Several times, when Quagmire's RV is shown moving, it is going forward, but the wheels are not moving.
When Stewie travels back to Chris and Vanessa's wedding, Meg looks exactly the same as in the present. Since Stu said she changed genders in college and would have gone before Chris, since she's older, she should be Ron now.
At Chris's wedding, Peter's dad Francis Griffin is shown at the wedding, but Francis Griffin is killed in Season 5 of Family Guy and Chris was never married before Francis died.
Stewie asks whether Walt Disney has been defrosted in the future. In reality, Disney was never cryogenically frozen, he was cremated.