This sounds similar to the Paladin Danse bug.

I finished the Pickman Gallery quest. I cleared the whole building instead of picking up the note and leaving.

When I return to Hancock he does not acknowledge it and just gives me the dialogue options for him to join me as a companion.

Just as I side note I completed The Dig quest for No-Nose before doing the Pickman gallery. I did not side with No-nose Bobbi