Y'all need to go back and reread the valentines day chapter - he's literally never received a chocolate before, so he naturally assumes it's a mistake. For a second he entertains that it was kubo who gave it to him, then he bashes his head on the desk.
Kubo then dances around telling him that she gave him the cookie, which probably cemented in his mind that she did NOT give him the cookie. It's really easy to see how he thinks it was a mistake.
Honestly, considering that he thought, even if only for a second, that she was the one who gave him the valentines gift makes me think we'll get there soon rather than later.