“Back to the Pilot” was seen by 5.961 million viewers

Chris & Meg appear in this episode but Seth Green & Mila Kunis do not.
Chris has no lines and Meg has one line, voiced once again by Season One's Lacey Chabert

After Stewie & Brian fix 9/11 during their second trip to Jan 31st 1999, Lois enters the room and congratulates Brian on the Harry Potter book series.

It would be impossible for Brian to take credit for Harry Potter in 1999 since J. K. Rowling had already published the first 2 installments, ‘The Philosopher's Stone’ in 1997 & ‘The Chamber of Secrets’ in 1998.

In the footage from the plane of Brian stopping the terrorists he looks like the 2011 Brian when he should look like the 1999 Brian.

Also in an error in logic, Brian may have stopped one set of hijackers but it's highly unlikely the FCC would ground every plane taking off from the East Coast based on a lone message that ends with “Seacrest Out”. The other two if not all three planes would most likely still have hit their target.
(Granted this is using real world logic and it was apparently effective within the Family Guy world)

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

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.

The time that the Pilot Griffins wait for the ice cream store cutaway to finish is a bit longer than the actual cutaway.

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.

When Stewie and Brian are in the future looking at the living room, the pole of the staircase that Brian is holding suddenly becomes traditionally animated while the rest of the staircase remains computer animated.