When speaking of 'non-native phases', we usually mean some crystalline phases (which are as themselves 'native'), where the ubiquitous defects might be of the highest possible dimensionality, that is, they become 'volume defects'. And all the particular examples could be borrowed from the book by Peter Pichler, entitled 'Intrinsic Point Defects, Impurities, and Their Diffusion in Silicon', Springer-Verlag, 2004.
With this in mind the stability of 'non-native phases' ought in fact to be related to the stability of defects, which might be systematically studied - see, for example, the recent paper by S. Y. Chiam et al., it is entitled 'Investigating the stability of defects in MoO3 and its role in organic solar cells', and published in 'Solar Energy Materials and Solar Cells', vol. 99 - Pages 197-203, Year 2012.