In the "Escape to New York" arc, the Runaways' ally Dagger is attacked (and possibly sexually assaulted) by someone impersonating her partner Cloak. And it turns out that the culprit was a hospital orderly who had access to her room...
During the Civil War tie-in miniseries, SHIELD declares war on the Runaways (because the agency's been taken over by Maria Hill.) In their opening salvo, SHIELD shoots up Victor, tearing his body apart in a horrific manner. As a follow-up, they send a genocidal alternate-universe Kree soldier who snaps Xavin's neck and then captures Xavin and Karolina, as well as Wiccan and Hulkling of the Young Avengers, and sends all four of them to a black site where they're tortured in front of each other by a fat, ugly, mind-rapey creep.
In the "Live Fast" arc, Chase temporarily turns against his teammates in an effort to resurrect Gert. The scary thing is how competent he was at being a villain, easily hobbling Nico and Victor and leaving the rest of the team scrambling to catch up.