Goofs

When Stewie is taking the dead Brian back to his return pad, it leaves a trail of blood, when the camera angle changes, the blood is gone.

Peter is seen standing in the shot in front of Joe's door, but vanishes when the group ponders the Brian with its throat cut.

When Brian and Stewie go back to the past to stop Brian from telling the 1999 version of himself about 9/11, one of the Brians denies having the idea to which the other says that he had the idea a few seconds before and his tail is still wagging because of it. However, in the previous shots, his tail was perfectly still.

At one point of of the future Brians and Stewies come back with Peter. In a following wide shot, Peter is missing, but then reappears a few seconds later.

When all the Stewies and Brians vote on making 9/11 happen, the Stewie counting gets an odd number of total votes, and Brian comments that is should be an even number. But Peter came back on one of the time machines and voted which actually makes an odd number of total people. One of the Brians died, making the total an even number, but that isn't revealed until after Brian says something. What makes this even more confusing is that the sole Peter who was present voted for both sides, and it is not made clear if the Stewie with the deceased Brian voted for 9/11 to happen or not. Finally, the leading Stewie could have not counted their own vote, flipping the vote parity once again.

One Brian wonders how the 9/11 vote can have an odd number of votes since all of the Brians and Stewies are traveling in pairs. One pair brings Peter along and we see Peter voting, thus the vote tally would normally be an odd number. But Peter actually votes twice, so the total should still be even. It turns out though that one of the Brians is dead and couldn't vote, so an odd tally is correct.

After all of the Stewies and Brians have arrived at the house and start arguing, just after the shot pans past the barber poles, one of the Stewies' feet are missing.

After the second Stewie and Brian go to stop the first Stewie and Brian from telling the 1999 Brian about 9/11, Stewie finds out that Brian then told his 1999 self about Harry Potter and became the author of the novels. The first Harry Potter novel was published in 1997, two years earlier.

When Brian and Stewie are in the past talking to the Kool aid guy, Brian asks where they can buy batteries....Brian has lived there a while and should know where batteries are sold.