Update: the following was written for version v.0.16a and is no longer valid with the current version.
yep it was the whole thing about the way she said she made a mistake....oh not the imprisoning part or the experimentation part, that was all good of course. but the part that she thought Killigan was safe when he was not, THAT is the thing she feels sorry for......and killigan just forgives her.
maybe the writer thought it would show killigan good nature, but in reality it makes him look like someone who just doesnt care as long as stuff like this doesnt happen to him again.
And now she even got "best character" as a Lab assistant ,destroying any hope i had that he would become a party member or that he would appear more often in the future. .....ok,maybe i am holding a little grudge about the last part, but the rest still stands.