<p>This paper argues that nonstoichiometric crystalline materials challenge composition-based accounts of chemical substances, and that a pluralist, function-centered ontology is required. The paper proceeds by establishing empirical challenges, developing a causal framework for vacancies, distinguishing entropy-driven from information-driven defects via mutual information, and defending a pluralist ontology with three logical types of chemical substances. Drawing on examples from solid-state chemistry doped silicon (Si:P), iron-deficient wüstite (Fe_1−xO), and oxygen-deficient titania (TiO_2−δ) I show that defects such as vacancies and dopants are not mere impurities but constitutive features of material identity. I distinguish between entropy-driven and information-driven defects, providing an operational definition of the latter in terms of high mutual information between microstate configuration and macroscopic function, grounded in causal specificity (Woodward, <CitationRef CitationID="CR47">2010</CitationRef>). I develop an account of structural causation, drawing on interventionist theory, to explain how vacancies exert causal influence without acting as efficient causes, while explicitly rejecting reductionist interpretations of the Hamiltonian formalism. I address three objections: (i) function as context-dependent, (ii) reduction to condensed matter physics, and (iii) the boundary problem for kind individuation. The paper defends a pluralist ontology with three logical types of chemical substances, grounded in a homeostatic property cluster account (Boyd, <CitationRef CitationID="CR5">1999</CitationRef>) and tailored to contemporary defect engineering.</p>