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.
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.