1. Lost quest - if you decline a quest (in my case I was still just a few turns from game start and too weak for to take on the mobs) the quest icon vanishes. It should remain so you can come back when you are able to do the quest.
2. I lost all my cities to the AI and then couldn't move any of my units. If they can capture them, I presume I can capture them back? I had my sov and uber champ right next to my last lost city and couldn't do anything about it.
3. Combat loop - my Sarus brothers initiated a killing blow from their reinforced tile onto an air elemental and the action went into a continuous loop. The only way I could end the combat was to press the auto-resolve button.
4. Game seems to get very sluggish in tactical combat after a few hours play.