The door knocked Brenner out. The phrase begins as a false lead so the audience thinks it was El. Then as El remembers she thinks it was her, this makes the audience sure it was here, then it is revealed that 001 did it. I think the confusion comes from the step by step reveal, more so than the actual circumstance. I think If Brenner seen the way the kids were killed he would know that she let 001 loose. His MO was breaking limbs and pulling there eyes into their heads. So I think it is 3. Brenner does a fll crossword in like ten minutes, so he's a sharp guy.

A cool detail, he pulls their eyes into the heads of his victims, ie, into their own minds, that is kind of an analogy for showing them their own minds, which is how he torments his victims.