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?
Plot hole: Vaughan discovers Lauren is a mole when he goes through her briefcase and discovers the wig, gun and fake passport she used in Germany a few hours before - surely even the worst secret agent in the world would have enough sense to get rid of such incriminating evidence as soon as possible, and not carry it back to the USA (sneaking it onto a plane, presumably) and leaving it in the room where the man you're lying to sleeps. Lauren is a highly skilled agent, if the Covenant selected her for a mission this important, so it's out of character (without an explanation) for her to be so sloppy.
Chosen answer: It does sound overdubbed, but there was no change in the organization. UCO is United Commission Organization. There are signs when Patel is coming that say UCO so obviously it wasn't changed.