Why did my newly captured Zone stay red?

A newly captured zone stays red because its morale is still very low and there is a chance it may revolt at the next daychange. The red highlight does not mean an enemy unit is present, it simply indicates that there is a revolt risk. The red flashing continues as long as the revolt chance is above 0%. Once you place enough land units in the zone center to reduce the revolt chance to 0%, the red flashing will stop.