These organisms are cleaning out an eye socket infection
can a broken unit on the first floor of a building shared with unbroken enemies in same location (got there via humanwave) rout away to the ground floor without being taken prisoner? does the CC token prevent rout?
Yes, as long as it is not under a Melee counter, a broken unit in the same hex as an enemy unit can rout away. See the line in the middle of A10.51 to the effect that a broken unit may never move ADJACENT to an enemy unit unless in doing so it is leaving that unit's location.