I'd been wondering about her father for a while, but the fact that Chise points out that her father looked happy before he left seems like a glaring issue. Maybe he was coerced or blackmailed into leaving by someone? Or maybe, if we assume his ability to ward off mystical creatures is from a clan he was formally a part of, perhaps someone threatened to hurt his family if he didn't return from wherever he came from? Whatever the case, it seemed like his son, who ended up inheriting his abilities while Chise didn't, had something to do with it. I'm wondering if it'll be addressed at some point, although if it's not then that fine. At this point in the story it's not really that important of a plot issue that it needs to be resolved anytime soon, if at all.