Some abilities in Magic care about specific amount of damage and others care about the sources of damage regardless of the amount. Abilities that prevent damage and redirect damage are obvious examples. For example, compare Shieldmate’s Blessing and Auriok Replica. Shiledmate’s Blessing prevents a specific amount of damage and Auriok Replica’s ability prevents all damage from a specific source. (They also differ in what they prevent damage to, the Blessing can prevent damage to a creature or player, Auriok Replica can only prevent damage to its controller.)
While Nested Ghoul‘s triggered ability does not prevent damage this ability does function similar way to Auriok Replica’s in that it does care about the sources damage. Anytime Nested Ghoul is dealt damage it’s ability will trigger and this ability will trigger just once per source. So if a Nested Ghoul is dealt four points of damage by one source, then the ability will trigger just once.