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: 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.
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.