That's not a bug. People asked for a more challenging experience and they got it. As you found out, you CAN kill them, but you need to be paying attention, not just bebopping around.
Can't win for losing with this crowd.
That's fine. If they want to do that and give out phat l00t early in the game I won't complain. I'll just go get myself trained in power armor (mod I have installed) and then I'll wear that near perfect condition Enclave armor.
I just nuked his ass after I reloaded. I had places to be, people to kill and couldn't be bothered by him at that time.
Found another one under an overpass. I happened to be on the bridge and under cover so I just snipped him.