robot expert.
just shut'em down.
or make them fight for on your side, or explode, if they drew your nerves
edit: shut down a hacked assaultron dominator at breakheart banks, was still there after the muties had respawned and, when i approached and the new muties attacked me, it woke up, un-stealthed right among them and turned them into tato mush )
Sounds like a little glitch out. If you have a good save before the mission try redoing it. If you don't have a save from before try running far enough away to reset the cell and then going back.. hopefully that won't fail the mission but I have no idea. Whenever I had little glitches like this a good old fashioned restart seemed to fix everything.