Lilpip was referring to thing they did opposite they're element like Applejack lying or Pinkie Pie being sad. In Fluttershy's case it was her mental breakdown at the Canterlot gardens when the animals ran from her. She got mad opposite her element of kindness.
Yes, these are basically the main cast. You should read it, despite all the gore and sexual content that usually dissuade me from reading fanfics, this one went way beyond making up for it with an amazing story.