Had a funny little thing happen to me just yesterday. I wandered into sunshine tidings co-op and it had a pre-built city plan I wasn't there to attack it or anything just passing through on my way to attack the raiders at the stockpile. While I was passing through a civilian came up to me and gave me the radiant quest to go rescue someone from the settlement, I thought alright should be easy ... then I saw the name of who they wanted me to rescue, "Feral Ghoul Roamer" luckily the quest sent me to the stockpile which I was already headed to. When I got to the ghoul I couldn't interact with it at all and could only just kill it instead and force fail the quest. I haven't tried to get this to happen anywhere else yet but I think this could probably happen at any settlement you would normally need to kill enemies to claim.