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.
Continuity mistake: In this episode Nadia Santos tries to find out who's the baby that her mother Irina Derevko is holding on a picture. She first shows it to Jack Bristow and later to Arvin Sloane. Later Jack asks to see to picture again and tells Nadia it's Irina's niece. At the several moments the picture is visible the picture is flipped, showing the baby on the left arm or right arm of Irina. (00:29:55 - 00:36:35)
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?
Continuity mistake: In 'The Abduction', when Sydney shuts down the traffic lights Sark's car is in the middle of the gridlock. When Sydney is fleeing with the stolen briefcase seconds later Sark pulls up beside her to save her, but how did he get out of the huge gridlock?
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.
Factual error: When Sloane is talking to Emily on the telephone, Sloane's phone emits a call waiting beep and the camera focuses on the phone's screen. There are two factual errors here: 1) The phone icon for "Line 1" near the top right hand corner of the phone display is in the "on-hook" position indicating that there is no call in place. 2) The call information is displayed incorrectly. It is obvious that this is a Cisco XML card with the text entered. (00:32:10)
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.
Character mistake: In season 4 episode 13, "Tuesday," when Marshall is meeting with Ulrich, he is both able to understand and reply in German. In season 5 episode 15, "No Hard Feelings," Marshall almost misses the opportunity to change the street light from red to green, because the text is all in German. Jack has to tell Marshall which word is green, indicating that Marshall does not understand the German language.
Other mistake: When Jack logs into Lauren's e-mail account, for one, the birth dates on Lauren's IDs say 1959 and 69 (which would make her either 33 or 44). Plus you can see (possibly) real e-mails from actual crewmembers, for example at the bottom you can see "FW:Photos for Alias Ep.#315." (00:10:57)