Sometimes I get confused about the purpose of a certain character's actions – for the reader. When characters do something radical, unusual, or questionable, I wonder if the author is advocating their choices, or if they are teaching a lesson through them. Sometimes it can be neither, or both. Many authors set up characters as examples for us to identify with and to follow in their footsteps. But other times, the character's choices are not as honorable and are simply meant to make a point. Other stories even set up the entire book as a metaphor, or as a clear depiction of "what not to do".
How are we always supposed to tell the difference? Usually, the author will try to make the distinction clear. With some stories, it is harder to spot. The most important thing to me is always consequences. What happens because of a character's choices? Some stories that are set up to tell negative character arcs spell out with the catastrophic consequences why the character had set their course toward destruction.