Not all of the map is under the control of a gang. Neutral areas remain uncoloured.
It's been said that the deepness of the colour indicates how much resistance will be given when CJ tries to take an area.
If CJ fails to respond to a counterattack, he loses influence and the area may go Grey.
I have noticed that frequently if CJ is 'wasted' during the third wave the Game will give the zone to CJ anyway. And, sometimes he has to hurray back to continue the fight. On a rare two occasions the foe gangs were waiting, at the hospital, for CJ when the hospital released him.