I have the new hotfix installed. I started the game over with a new character. I follow the Vagabonds to their hideout, get the med kit. Then make my way to their headquarters. I help fighting the IOD's until the fight is over. Now they act like they don't know me. I did get Yvette to heal my injury. I go back several days later to the tavern and they are still in a circle, with guns drawn. Everything in the tavern is available to take, so I take everything available.
Seems I'll be looking for another faction to join now.

did you find and terminate the Dog radio spy in nearby diner/bar?
This quest should be available right after you talk to Yvette.

She just healed me and I can purchase items from her, but she doesn't offer a quest.

If they have still the weapons out the script still "sees" some of the iods somewhere. Stuck in the building or glitched inside a wall.

Yvettes trading/healing script is seperated from the quest process, she would heal you mid-fight.

They are probably stuck in the wall. There isn't any red squares, which would indicate hostile IOD's I will make one more check on all the floors. Joining the Vagabonds was my goal, but there are other factions to explore.