Inspired by the previous finding of some unusual vapour/liquid nucleation results on the ternary water/n-nonane/1-butanol system, atomistic simulations were carried out for a detailed investigation of this mixture. These simulations reproduced the experimentally-reported non-ideal nucleation behaviour for this system, including both onset activities and the average compositions of the critical nuclei. Close examination of the nucleation free energy data and the structure of the critical nuclei reveals two types of phase separation. One occurs internally inside the clustervia formation of a multi-layered structure. The other takes place externally, leading to the coexistence of multiple nucleation channels, characterized by critical clusters of different compositions. Such mechanistic and structural heterogeneity is the microscopic origin of the complex nucleation behaviour observed for this ternary mixture.