Many naturalists and materialists (not the same thing) favor reductionism over emergentism. Emergentism, some of them say, is a like having a magic wand that can simply declare higher levels of phenomena without having to really explain them; they just "emerge." But just like with scientism, there are strong and weak versions of emergentism. The quote below is from Sean Carroll in a Q & A he did with 3 AM magazine on what weak emergentism is, and why naturalists shouldn't fear it.
I think emergence is absolutely central to how naturalists should think about the world, and how we should find room for higher-level concepts from tables to free will in a way compatible with the scientific image. But “weak” emergence, not strong emergence. That is simply the idea that there are multiple theories/languages/vocabularies/ontologies that we can use to usefully describe the world, each appropriate at different levels of coarse-graining and precision. I always return to the example of thermodynamics (fluids, energy, pressure, entropy) and kinetic theory (collections of atoms and molecules with individual positions and momenta). Here we have two ways of talking, each perfectly valid within a domain of applicability, but with the domain of one theory (thermodynamics) living strictly inside the domain of the other (kinetic theory). Crucially, the “emergent” higher-level theory can exhibit features that you might naively think are ruled out by the lower-level rules; in particular, thermodynamics famously has an arrow of time defined by the Second Law (entropy increases in isolated systems), whereas the microscopic rules of the lower-level theory are completely time-symmetric and arrowless.