In the recent years, attempts to relate metaphysics and sciences have taken various alternative forms such as metaphysics applied to science, metaphysics of science, and scientific metaphysics. In this article, I focus on scientific metaphysics and specifically explore the challenges with developing ontologies through four arguments. The Argument from Representational Indeterminacy highlights that global ontologies fail to clearly identify their target phenomenon. The Argument from Independent Inaccessibility explores the methodological difficulty of accessing a world that is independent of specific sets of phenomena. The Argument from Conceptual Mismatch focuses on the tendency of local ontologies to pick out arbitrary scientific concepts, adapting them to study phenomena where they might not fit well. Finally, the Argument from Eliminative Prophecy details the possibility that local ontologies could eventually be rendered redundant by mature versions of scientific theories. In the end, given these challenges, I recommend an eliminativist stance toward ontology development.