I have seen that a few times.
AFAICT this appears when a civ collapses and their slot is reassigned to another one. While they collapse the tiles in the fog of war of a player's map are still bound to a certain player (?) ID. When that is reassigned the colour will change to the new civ, as that one now has the same ID.
A possible fix would be to clear all culture of a team from all player's maps, even in the fog of war, when they collapse.