Unofficial Fallout 4 Patch

Game version: 1.8, no mods at all and no UFO4P.

Faction relation at the start of the quest: BoS friendly, RR friendly, Minutemen friendly - was targeting the MM ending. Institute obviously friendly because of the quest.

What I did:
Informed RR, but not BoS.
Met with Courser, and went inside as fast as possible. The Courser fights both BoS and RR, Player does nothing - remains neutral and is not attacked by anyone. Settlers cower and are not attacked.
Inside cell (cellar) - like outside. RR turrets also friendly to Player.
After reaching the synths Player was asked by them to free them or leave them be in peace. Player agreed to free them and the Courser became hostile - new objective 'Kill the Courser'.
After killing the Courser - next objective 'Deal with the Synths'. This was not possible, since it was already done, all dialogues with each on of the Synths were only standard responses. Did not accept the bribe before Courser became hostile.
But killing the Courser also started a new quest: "Meet Father at CIT ruins roof". While combat still was in progress Player left Bunker Hill. Player remained neutral and was not attacked.
I decided to end the Institute quest line here. Is not strictly necessary, but possible. So I was unfriendly to Father and left the Institute. Quest "Kicked out from the Institute" started.
Faction relations after this: BoS friendly, RR friendly, MM friendly, Institute hostile.

In the Pipboy the quest 'Battle of Bunker Hill' was shown as done. But the objective 'Deal with the Synths' was never reached.

Situation in Bunker Hill after being kicked out from the Institute:
BoS soldiers still present, attack RR agents, also still present, when they see each other. RR agents attack caravan guards (seems to be Docs caravan). BoS soldiers present long after end of the main quest (Institute vanquished with the Minutemen). BoS troops quite superfluous and inactive, but make comments and can be talked to, with standard answers.

Settlers and caravan personnel all keep cowering in fear, but can be interacted with normally. Settlement can be won, if the quest for the mayor was done before. Settlement works normally, but all NPC animations are off, NPCs keep cowering. Fast traveling, save & load, game restart does not change this. This persists even after the end of the main quest (MM ending).

The cowering can be fixed with the console:
Enter 'stopquest ef21c'
Then go to a closed cell. Wait 24 hrs.

This fix works, it seems to stop the state 'Battle of Bunker Hill', which was loaded at the beginning. This quest state is never stopped. But it does not fix the remaining NPCs (BoS and RR), the synths remain in the cellar indefinitely, the RR agents there too. So I think, either it was thought that all BoS and RR would be dead at the end, and no cleanup was added, or there is a cleanup which is not done properly, maybe because of Player being friendly to both, BoS and RR. This includes missing cleanup of cowering NPCs (Battle State for Bunker Hill), which is clearly a bug.

Should be easy to see, and is reported on the Internet - many people had this situation. If one does not (or cannot) use the console fix, the NPCs in Bunker Hill cower until the game is ended.

I think, not only the cowering should be fixed, the Bunker Hill NPCs should be cleaned up too. The bodies of killed RR agents and BoS on the outside disappear, so maybe there is no quest running in the background, they are removed because their aliases do not belong to a quest. So maybe it was intended this way. But the cowering is clearly a bug.