Not entirely sure if this is a bug or if it was a deliberate design choice, but all the minions in the Empire prisons are Empire-controlled, rather than being player-controlled or neutral as is normally the case. This means that upon capturing a prison nothing happens, and the captives remain imprisoned. This doesn't make much sense in terms of either story or gameplay, and is kind of at odds with the narration for this part of the level (dlc1_campaign4_narrator_line9: "It appears they have imprisoned many minions. Release them, Underlord, and revel in the city-sacking consequences!").
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