One bird might accidentally snap its neck in a fight or fall--two? plus another injury? Something got to them. I can't say whether it was a human or something else, but hte fact that they now run from you makes it sound like it likely WAS a human. Woken up at night by a human they would have run to, they likely would not have done much flapping. Sprinkle flour or powder on the coop floor and all around the coop and fun. This will show footprints and tell you what was there. As has been stated, get a lock for the door, and do talk to your neighbors--I like the way it was stated--expressing concern that they may have had losses as well--and watching to see their reactions. A night vision camera that runs on a 24 hour loop would be good for identifying the predator. You might also place motion sensor lights and/or alarms near the coop.