I had a weird glitch kind of related to this. Earlier in the game Hancock asks you to go investigate the Pickman Gallery. I left that task on hold for a while, and ended up completing 'The Big Dig' which is the quest where Hancock becomes available as a companion. A while later I did end up going to the Pickman Gallery, but I was unable to complete it afterward because when I talked to Hancock only the companion dialog was available. Quite some time later I did the Silver Shroud quest and I brought Hancock along because I figured he could appreciate cleaning up the streets of Goodneighbor (this was before I knew he became a part of the quest). I killed the first few people, and then got the optional 'Assassinate Kelly Tiller' portion. I went to the National Guard Training Yard, found her uninteresting, and killed her. I got a message saying 'Hancock hated that.' Usually I'll reload after this happens, because I'm currently still trying to max out Hancock's affinity. However, I talked to him right after killing her to get his thoughts, and he said "When I asked you to go to the Pickman Gallery, I never thought you'd bring me with you!" and then the Pickman Gallery quest completion was triggered, I was paid, and it was cleared from my log. Afterward I was able to finish the Silver Shroud quest normally. This was odd. He said "I never thought you'd bring me HERE" as though we were at the Pickman Gallery...but we were at the National Guard Training Yard.
Obviously I don't think this offers any kind of solution, but this portion of the game is definitely bugged somehow. Hopefully it gets addressed.