When Stewie and Brian return to the present and it is revealed that Brian stopped 9/11, Tom Tucker mentions an AZ football player named Pat Tillman being tackled by his own team. In reality, Pat Tillman was a football player who joined the military after the 9/11 attacks in support of his country. In 2004, Tillman was killed in a friendly fire incident, thus being killed by his own team.
The first thing Stewie says when he looks through the window of his 1999 home is: "Oh my God what's wrong with Meg's voice? She sounds like someone who's about to give up a huge opportunity." This is a reference to the fact that Meg's voice was originally done by Lacey Chabert for thirteen episodes before Mila Kunis got the job in the episode "Da Boom" and played the part from that point on.
During their first trip back to 1999, Stewie makes note of two production errors that occurred in the pilot. The first was when Peter's eye goes over his nose when Lois reminds him about the time when he got drunk at church. The second was that, when Peter and his friends are drinking at the stag party and watching TV, the TV isn't plugged in.
American Airlines Flight 11 is the flight that Brian takes and stops the hijackers on in this episode because in real life, this is the flight that show creator Seth MacFarlane missed boarding on September 11, 2001, having arrived late due in part to a hangover and an incorrect departure time from his travel agent.
While all of the present day and future scenes are animated in 1.78:1 (16:9) widescreen, all of the 1999 scenes are animated in 1.33:1 (4:3). This is because the events shown in the 1999 scenes are from the first episode of Family Guy, entitled "Death Has a Shadow", which was originally animated in 1.33:1.