Perhaps these 'missing members' are not missing at all! Maybe there were more then 13 members, but they called themselves that to mislead their enemies! Perhaps, this whole time, these missing members have been hiding amongst the NPC's, watching Sora, just waiting for the right moment to strike.
There is a solution to this though. To be utterly sure Organisation XIII is wiped out... we have to KILL all the NPC's! WE MUST CLEANSE THE NON-BELIEVERS!
-beats Cloud to death with a bloody, disembodied Moogle Pom-Pom-
They...all... they all must die! DIE! AHAHAHAHAHA!