[Sackett]

I would point out that Mikoto has repeatedly show that she does not trust authority. Instead she prefers to take care of things by herself. Hence her hobby of trolling for punks to punish. That's been a consistent part of her character from her first introduction in both Railgun and Index.

On the other hand, Mikoto has consistently show herself able to ignore unpleasant realities that don't currently intrude on her life. She's a good tactician, but she's not a strategist by any means. She lives in the now, and though she is intelligent enough to recognize that something isn't right in Academy City, (her musing on why there are so many thugs in the City despite it's superior technology), as long as it's not right in front of her she can satisfy herself with protecting the interests of herself and her circle of friends.

It's one of the reasons the Sisters and the Level Shift experiment hit her so hard. It's completely the type of unpleasant thing that Mikoto wants to ignore and pretend isn't going on, and yet she couldn't. The Sisters had her face, and her DNA, and they called her sister, and they were being killed. It was just too much for Mikoto's usual cognitive dissonance to handle.