An obvious problem with a materialist understanding of the world is that we have subjective experience and can’t begin to imagine what a materialist explanation for subjective experience would look like. What do atoms and the void have to do with our sensation of redness, as opposed to redness as a wavelength of light, type of event in the brain, or behavioral tendency (e.g., a human tendency to say “that’s red”)? Electromagnetic waves or brain chemistry might somehow cause our sensation of redness, but they can’t explain it completely because it’s basically different in kind. It would be like an explanation of the existence of the solar system in terms of double-entry bookkeeping.
Presumably materialism could be extended to cover subjective experience, just as tic-tac-toe could be extended to include nuclear physics. If it were, though, there would be no apparent reason to call it materialism. Materialism is not an understanding of the world, because there are things it gives us no possible way to understand. At most, it’s a research program, a statement of intent to explain as much of the world as possible in materialist terms. That’s OK, of course, but why confuse a research program that has obvious fundamental limitations with truth or rationality? When we talk about things the program won’t deal with why treat that as an illegitimate invocation of “the God of the gaps” or some such?
The gaps are real and they’re not going away, and we have the world as a whole to deal with. Things become important to us by virtue of their connection with subjective experience, so a procedure that can’t deal with subjective experience can’t be more than a subordinate aid in deciding what we should believe or do. Many people seem to think it’s rational to treat materialist science and its imitators (like the value-free social sciences) as our only source of objective guidance. You might as well think that of the phone book.