Craft a bell then ring it. They'll all come to the bell then you can get into workshop mode and re-assign them to wherever you want them to go.
Have you finished the MQ? I think I've seen this behaviour in videos from people who had finished with a single (evidently "wrong" for Bunker Hill) faction...maybe BoS?
I've just finished setting up my all endings save, so can't tell you for certain just yet.
i tested it, this is what i did, and i did this a few times to check, it seems that if you initially go against "father" then when you get back to bunker hill after the battle everyone is crouched down, if you initially side with him and wait for him to go back to the insititute, then kill him or someone else in the institute, become hostile, then go back to bunker hill then the people will not be crouched, i tried to tell him i didn't want to be part of the institute when he was outside on top of the MIT building after the battle of bunker hill but every time i did that the people at bunker hill were crouched, so i tested this like i said and initially went along with him [during the conversation on top of the MIT buillding] and waited to break away from the institute until after he went back underground and then i went and became enemies with the instuitute and when i went back to bunker hill the people were ok and not crouched down, i did this a few times to double check, so i'm not sure why it is that if you become enemies with the institute while he is on top of the MIT building makes the people crouch but it seems that it causes that, so you need to not become enemies while he is on top of the MIT building, wait until he goes back to the institute then you can become enemies with the institute and the settlers won't be crouching, so you might need to replay the battle of bunker hill but thats the way to fix it, there may be other ways to fix it but nothing else worked for me. i'm on the xbox
just do it how i did it, you don't have to side with the institute, but after when you get the message to "go talk to father" on top of the MIT building, "don't becomes enemies at that point with the institute", if you tell him you are going to be against them while on top of the building all the settlers will be cowering whehn you go back to bunker hill, so go along with him for the time being, then go back to bunker hill [you'll see everyone is normal and not cowering] THEN go back to the insititute and become enemies with them, i just killed someone and then went to the emergency relay station and left, thats how i got around the cowering issue, i tried lots of different ways that didn't work and i read where someone said the same thing i told you, that if you become enemies while on top of the MIT building talking to father it glitchees bunker hill somehow and they don't "uncower", i test this a few times and if you become enemies with the institute while talking to "father" on top of MIT after bunker hill the settlers seem to remain cowered, i wateed days and that didn't help, so finally i worked around it and waited till after father goes back to the insititute and then became enemies and that keeps it from glitching. once you become ememies with the institute while talking to father on top of the MIT building its too late to fix.
Try thoroughly exploring the area around Bunker Hill, including the cellar that you go into during the Battle of Bunker Hill. I had this happen, and it turned out that there was a stray synth wandering around a block or so away from Bunker Hill. Once I killed it they all stood up normally.
The other option would be to just reload an earlier save and see if the same thing occurs after playing through the quest again.
You ask what people do.
I have the cowering bunker Hill residents.
I can still interact with them and trade with them while they cower.
So I ignore the cowering.
I have built some market stalls and brought in my own non cowering residents.
Now the game is over I have been toying with the idea of surreptitiously killing the Bunker Hill residents that can't be traded with and hiding their bodies.
I've done similar at Covenant.
Got rid of the old man who does the mime act, for a start
That's true.
I wouldn't normally do that but in this case I consider it a workaround to squash a game bug.
I don't know if this works with v1.4 since I haven't gotten that far yet in my latest play through, however at least up to FO v1.3 on PC you could use this console command to stop the NPCs from cowering.
stopquest ef21c
http://fallout.wikia.com/wiki/The_Battle_of_Bunker_Hill