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.
Plot hole: When Sydney is visiting Will in jail, she says that the CIA changed all the passwords. However in a later scene, Weiss asks will for his password, and Will says that it's "Sydney." If the passwords were changed, wouldn't Will's have been changed too?
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?
Revealing mistake: During the episode "Double Agent", Sydney and Vaughn are at her apartment, cooking dinner. Sydney reaches into the "hot" oven, without an oven mitt on.
Factual error: When Sydney goes to find the Artifact in Siberia, she is told that if the ice breaks she will have only 4 seconds to get back up. If it is that cold out how come the ice is not thicker?
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?
The Getaway - S2-E12
Other mistake: When the bad guys are searching the database for facial matches with Michael Vaughn, it shouldn't take them very long, as there are only 5 or 6 different faces that flash up on screen, just repeated over and over.
Continuity mistake: At the start when Sydney is being held and talking to Khasinau, there is blood coming from the corner of her mouth. At this point it reaches the bottom of her chin, but moments later when she is talking to her mother, the blood is noticeably shorter.
Passage (1) - S2-E8
Factual error: When Sydney goes to Uzbekistan, it isn't Uzbekistan. The restaurant where the meeting occurs has nothing made by Uzbeks, and it is too remote to be made by foreigners. 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: In Season 2 episode 4, in the scene after the house explodes, Sydney can be be seen communicating with the CIA over her COM unit. In the proximity that she was from the explosion of such a magnitude, COM frequencies are disabled. (00:40:35)
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.
The Getaway - S2-E12
Character mistake: When Agent Vaughn's identity is discovered while on the date with Sydney, it's matched via his driving license, gym membership card, and library card. The driver's license has his name spelled incorrectly (Vaughan instead of Vaughn). (00:24:02)
Continuity mistake: Ariana Kane finds out about Jack's murder of Haladki through analysing the brain matter from the pistol he used to kill him. However in the episode 'Almost Thirty Years', Jack shoots Haladki in the neck, not the head.
Answer: Bad Day by R.E.M.