In the Gensokyo 20XX series, we have this to somewhat the case with Mokou who is nicknamed "Huzi", being that her last name, Fujiwara, is alternatively pronounced and spelled Huziwara, leading for her nickname to be Huzi and she is usually referred to as such. Apparently, an age-regressed Reimu thinks her first name is her last name.
At least one Mass Effectjustifies Commander Shepard only being called by their rank or last name by explaining that no one (Shepard included) actually knows their first name.
Chiyo Ueda, Arata Miyazaki, and Kazumi Katsuya of Despair's Last Resort all do this. Chiyo does it out of politeness, while the other two out of rudeness. Chiyo makes an exception for her Childhood Friend Kumiko. After Shizuka's death, Kazumi refers to her by first name. Arata calls Takara by her first name after she figures out his crime, but it doesn't last long since he gets executed.