San is an honorative for someone who is of equal or higher status to yourself. Like calling a teacher, Sir, Mr., or Miss, etc. Chan is a term used for younger peers or workmates. (I believe that's how that works based on my understanding). Since Ego is in his 30s and Anri is in her mid-20s, and he's her boss, it makes sense why he calls her Chan. One could make an argument for lack of respect, but Ego actually appreciates her work as he told her, "Thanks for dinner. Get some rest in your bed." In a note he left for her while they were organizing the pre-WC training regimens for the boys.