Other mistake: For secret agents, Sydney and Dixon are not very dedicated to secret identities. At several points they refer to each other by their real names in front of other people while they are under aliases. Examples include The Confession party and The Coup Las Vegas scenes.
Other mistake: Near the end of the show they are supposed to be in a parking garage in Spain, but there are way too many American cars.
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.
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)
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.