@captain_crunch Mikoto (the perv who always try to lewd Rin) was the one who made the box, and yes, Togeta and Rin's family worked together to trick her that.
As for Ikuto's deduction, he merely used reverse physiological to narrow his suspects (to the ones that seemingly couldn't have made the box), and the fact that there are some unusual food inside that box when Okome found led to his conclusion that it must belong to Mikoto, who's off the Shinobi clan that could be connected to said food.