Omegawolf said:
Hey Killap. I'm afraid I've had more problems with running NPCs. I decided to kill all the squatters in the orphanage. I locked both exits and started shooting. One of them still escaped through the northwest corner of the building that is hanging off the edge of the map. Now the quest remains permanently incomplete since I ended combat and saved before I went back to the corner I saw him run to to kill him.
That's not a bug, it's just bad luck. (or getting frustrated and hitting F6 when you want F5, and vice-versa)
I had the same problem at Slaver's Camp: one of those guys would always run off the map where I couldn't get him, and if you are too badass, they will NEVER wander back into range, like Radscorpions and Geckos will.
I solved this at Slaver's Camp the same way you are trying to do at the big building, by locking the doors first. If that doesn't work though, it isn't a fault of the script. It's meant to be realistic and 'Shit happens' so load a saved game and try again.
edit: (There are only 5 squatters in that building, 2 have a knife and one a crowbar! Only 2 doors also. No offence meant, but how was it possible for anyone to escape?)