According to Yomiuri Online, two men have been arrested for performing "improper acts" in hotel rooms with the same 12 year-old girl on multiple occasions earlier this year. The girl met both men, aged 49 and 36, through her 3DS. Yomiuri Online doesn't specifically mention SwapNote. A Mainichi News report, however, does.
Mainichi reports that charges for child pornography have also been filed against another man, 44, who had allegedly two girls - then aged 11 to 12 - send nude photos through SwapNote, or "Itsu no Ma ni Koukan Nikki" (いつの間に交換日記) as it's called in Japan. The man has confessed to doing so.