Angelina may have gotten sole custody over the kids, but Brad is still a part of their lives. He is allowed to continue being their dad and be around them because, well, he is still their father. This was something that especially meant a lot to Shiloh because she was so close with him. It meant a lot to her that her parents allowed her to be whomever she wants and that they never judge her for the way she is.
Because Shiloh has such a close relationship with Brad, it puts her in an uncomfortable spot. She still cares deeply for her mom and appreciate what she does for the family, but it is still very difficult for her to see everything people have to say about her dad. She knows Pitt isn’t perfect, but she also knows that it takes two people to make a divorce happen. She has documented everything in a journal and people think she might be ready to talk about what’s been going on.