The bug:
City-States remain allied to the civ that conquered them after being liberated.
The game: ver 1.0.0.20
I had attacked Rome, who had 2 *conquered* city-states. Due to my path of attack, I had left these 2 for last, so by the time I got to the C-Ses, Rome had been conquered and removed from the game. The first C-S, Helsinki, liberated and allied to me as I expected. The second, Monaco, liberated and allied ROME, the same civ that conquered them. However, since Rome was now out of the game and no longer at war with me, I was given the normal options of gifting gold etc. I was able to gift enough gold to overtake Rome's influence and become ally.
When I attacked Iroquois, they also had a conquered C-S, which I attacked early in the campaign. After liberating that C-S, they also remained ally to the same civ that conquered them, Iroquois. My influence with them was normal, 130ish due to the liberation bonus, but since they were ally to Iroquois, I was only friendly, and they were still at war with me. Because the Iroquois were still in the game, I was given no options for dealing with the C-S, no peace, no gifting, nothing. Just friendly influence while remaining at war.