Plot hole: In 'Phase One' Sydney tells Will during the day to "Get Francie and get out of town" because she realises there's someone after her. Later that night Francie is shot at her restaurant and replaced by Allison (the clone), but Will was supposed to have taken her away already. There's no question of him not finding her - the restaurant would be the first place he'd look for her.Shay
Factual error: Francie alters Will's cell phone so she can download items from the CIA's computers via it. In order to start the link, she calls him on the cell phone, asks him to look up a recipe on his computer, and then this cell phone is able to download a 3 gigabyte file. The phone Will uses has a maximum data transfer rate of 14.4 kbs; wouldn't Will get suspicious after he's forced to surf for this recipe for 57 hours while that gigantic file downloads?
Factual error: When Sydney goes to Uzbekistan, it isn't Uzbekistan. The restaurant where the meeting occurs is not anything made by Uzbeks, and it is too remote to be made by foreigners. The land around is also very lush, unlike anything in the deserts of Uzbekistan. The people are speaking Arabic, instead of Uzbek and Russian, and the sign on the wall is also Arabic. The guards are also wearing what appears to be a Russian uniform, even if the badge is correct.
Continuity mistake: When the new head of SD-6 invites the security agent to play back what Sloane wrote, the screen is already displaying the letter. We only see the entirety of this letter later, once the "playback" has been completed. It can't be that the boss has done it once already, as he's surprised to see the final text.Jon Sandys
Trivia: Throughout the show, the number 47 appears many times. There are multiple room 47's (where Syd found the Circumference in season 1 and the room in her memories from season 3, among others.), there are 47 Rambaldi artifacts, and page 47 of the Rambaldi manuscript was the page that had Sydney's picture on it.