I had 3 scouts in a city of my teammates when they quit. The city went neutral but my scouts remained. I didn't move them for a turn or two and then decided to see what would happen when attacked with just one. It went to war with the city and lost miserably (think there were 4 heavy cav or something like that). When the battle was over ALL 3 of my scouts had disappeared. The battle accurately only had one of my scouts in the fight. I didn't have a chance to try to move them off the city to see what happens.
Another weird issue which may or may not be related is I lost the game, bad. I got a message in game saying I lost and an email, but in the my games screen it says Game Won.