Retreat won't trigger during the "cooldown" time of the war, so it may be they were back above the threshold by the time it was checked. The Outbreak state shouldn't affect Retreat directly, though it would make it easier for them to gain influence from passing traffic.
There are also some other conditions which would stop a Retreat from starting - you haven't given enough information to absolutely rule them out, though they are unlikely.
- native factions can't retreat, obviously
- a faction can't retreat if it owns a "locked" asset in the system (a few lore factions and their megaships, basically)
- a faction can't retreat if it expanded into the system less than ten full days ago