The missions where you collect crates changed the behaviour - originally, when you interacted with a crate, a group of enemies appeared.
That annoyance is gone now, however they seem just to spawn with some significant delay - when I finished the mission I met on my leave a train of enemies that followed me through the map.
Happened in both G and I variants.
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I did the crates on both factions yesterday. One group of illithids spawned from an unguarded crate. I didn't have anything following me that I could tell. Mobs on those maps do tend to respawn as if they were overworld maps. Perhaps what was following you were normal respawns and the following bug was caused by something else?