So you know those warehouses that you have to fight arachnos around during the Aaron Thiery arc? well, after you finish that arc, from then on the game doesn't know what to instance or if to instance something special there. So when you approach the edges of the instanced arachnos controlled area all enemies such as clockwork, vahzilok or hellions disappear and auto-de-target until you leave the instance's buffer zone. Even auras will not harm said enemies in this buffer area. they also lose sight of you and go back to their spawn points.
It's a pain on kill missions (kill 15 clockwork "well I just got out of a warehouse here in atlas so.. ah damn they ran into THAT area after the first hit..")
I assume this will take a lot of work to fix without breaking the aaron thiery arc.. it should be as simple as adding some conditions onto the buffer zone "if player has mission from contact Aaron Thiery: trigger instancing. Else: pass. but CoH code probably has some other complexities.