Open soffit where roof hits the upper wall plate, doors that flex at top or bottom even when locked or latched, if raised off the ground holes in flooring, holes in walls, holes in roof, poorly latched chicken door, and predators in the coop when you closed it. Predators in the coop happens more often than one might imagine 
 
 
Any opening or opportunity to open large or small can be the entry or exit even through an open soffit space between roof and upper wall plate. 
I have seen raccoons climb through an un-screened ventilation fan housing 6 feet up the wall and 3 feet from the roof in a commercial chicken house by jumping. Kind of like a squirrel on a bird feeder. One never knows.
Fox, coyotes, mink, weasel, and even raccoons can all get into a killing frenzy. But mink and weasel are usually the worst in multiple kills in my experience. 
Hawks, owls, and birds of prey generally only kill to eat one at a time. I have hunted with birds of prey as a falconer and rarely ever see multiple kills as part of their M.O. but in predation almost anything is possible 
 
 
Sorry to hear about your loss 
