It seems intuitive to me to think that if there is a basic substance or building block of nature (e.g. fermions and leptons, etc.), then all facts regarding entities comprised of that substance are reducible into facts about instances of said substance. For example, the term "water" is reducible, on a chemical level, to "two hydrogen atoms combined with an oxygen atom via covalent bonds." In turn, this chemical equivalent of "water" is reducible to something like "two sets of identical combinations of subatomic particles combined with another unique combination of subatomic particles via [insert some atomic description of covalent bonds] (I'm no physicist)." I like to think that this process can proceed until we reach the most basic of substances, at which point we would arrive at the most primal description of a phenomena.
I think topics of the social sciences are subject to this as well. For instance, "a language" can be reduced to "particular sets of certain reverberations used in certain groups of massive collections of subatomic particles (people) who engage in brain states that correlate both/either artifacts of physical substance and/or brain states with some of those particular reverberations of sound." Obviously, you could go "deeper" in the analysis, but for the sake of time and my sanity, I won't try to do any better; you probably get the idea.
That was just my understanding of a typical reductionist project, but I have a feeling that I might have just conflated reductionism with physicalism. My question still stands, regardless: What are some of the problems with reducing natural and social phenomena into facts about the primary substance of which they are all ultimately made of?