why is mrs flynn treating charlie funny?

We aren't given a reason for Mrs. Flynn's fear, but we can infer that Charlie's increasing partying and avoidance of work might be the reason. She doesn't know what to expect from him.... he's been brought home by the police and avoids the bakery.

April 13 - Still didn't go back to work at the bakery. I told Mrs Flynn, my landlady, to call and tell hf. Donner I'm sick. Mrs Flynn looks at me lately like she's scared of me.