It sounds like your ally is somehow placed in your custom villain group as an enemy. Check your custom group to see if he's there.
For the enemy LT, if you want to fight just one of her. You're going to have to place her in another group, you can name them the same by saving to a different location, and pick "Defeat a Boss" from the mission objectives section.
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Golden Age Heroes
Thanks, Nurse M. I'll try and move things around.
Hmmm, I still screwed up somewhere. Oh well, back to the tutorials and guides....
I published my first arc ((174181, shameless plug)), but on my second one, I've run into some trouble. I added an ally to save and help me, but there seem to be some enemies that look just like him that attack me. There's only supposed the one ally to save. And my enemy lieutenant has multiple copies throughout the map as well. There are her minions in the map, but multiple copies of her as well. Anyone got any idea where I screwed up? I appreciate it.