You can only dock one ship at Coxen Hole. You can tender there as well so if you saw two ships, then one was tendering. Royal Caribbean also uses it. NCL was the 1st cruise line to have regularly scheduled trips there so NCL (I believe) has priority.
Mahogany Bay has a narrow channel and although one ship can usually maneuver there fine, getting the 2nd ship in can be a problem if it is windy or rough seas. Many times one ship will dock, but the 2nd ship scheduled will have to tender at Coxen Hole or miss the port.