I've cleared out the entire inside and I suppose outside of the plant yet it seems I'm still not done? I killed the female raider on the outside of the plant in the connecting bridge offices and the sniper at the top of the scaffolding. Did I miss someone? I'm following the compass but whether I go inside or outside the plant the numbers just countdown then start over.

Probably a bug.

Go back to a save before you got to the area.

You need to kill the leader; I think he's the only named raider - some jay name. He is indores somewehre just keep looking.