I have an idea. Sometimes, when you capture a capital city of a large enemy, it splits the entire enemy civ into two factions: a loyal faction with the same color, and a disloyal faction with a different color. Sometimes the disloyal faction is your own color, but frequently it's a different color. Say you are playing with seven civs, with one being the English, and you capture the capital of the Zulu empire, which is large and disloyal, and the Zulus split into the loyal Zulu faction and the disloyal Carthanginian faction. You would have two orange Civs. This is all hypothetical, as something like this has never happened to me before, just thinking of a possible explanation.