Kotaku reports that supposedly a few men have been using Swapnote to get in hold of young girls (kids) and asking them to do something naughty things.
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. This man has confessed to the acts.
Thanks to these guys for getting rid of one of the neatest/coolest things to do on the 3DS.