The second season premiere introduces Donal Logue as the detectives' new captain, as Crews and Reese chase down a serial killer that puts their victims in trunks.
Even when Charlie isn't doing something to cross over legal and ethical lines, there is always the smell of criminality about him, from being in prison, as seen in this clip:
And it's not just that criminals that think so, either. It's the police, his comrades in arms. And since perception often forms reality, how is Charlie supposed to resist being what they see?