The article analyzes some conceptual models of modern science, which border on metaphysics, that is, when working with them, they require an assessment of their ontological and cognitive status. The concepts of “dark” or “black” matter are considered in connection with the so-called problem of “mass defect”, and negative quantities in mathematics. Questions are raised about the nature and cognitive meaning of understanding the notion of matter within the framework of conceptual scientific models, which allows us to identify the cognitive grounds for using these concepts and their relationship with metaphysics. As a result of their analysis, the authors come to the conclusion that the system of the Universe has more than one direction of development, the movement of being does not go in a straight line, it is not one-dimensional, but s described by multidimensionality. Since this movement of being is volumetric and multidirectional, it is not possible to build a substantiated theoretical and cognitive model of objects with a completely opposite direction of development in complex, multidimensional systems with nonlinear development. The phenomena studied by science have a single ontological basis, which not only provides a close relationship between the conceptual apparatus of science and philosophy, but also allows us to assert that numerous concepts that do not have a fundamental cognitive status in science can and should be interpreted within the framework of metaphysical conceptuality.