Reductionism is the idea that the world can be understood as the sum of its parts. Objectivity is the idea that there is an external reality independent of our biases and measurements. Together, these ideas are implicit in much or all of science.
How could these go wrong? Maybe there is some supernatural phenomenon that is not amenable to scientific study. There could be emergent features that do not reduce. There could be objects that behave differently every time you look at them, without any pattern. Maybe you can reduce a system to particles, but find that those particles seem to still have some complexity, but cannot be reduced any further.
Quantum mechanics is a theory that seems to run up against the limits of reductionism and objectivity. Naive reductionism would lead you to reduce an electron to its charge, mass, spin, position, and momentum, but the uncertainty principle prevents it. Attempts at further reduction and realism have nearly always led to some hidden variable theory. However these theories have all failed. We may never reduce electrons to mathematics.
The subject of reductionism and determinism really creeps people out when applied to genomic influence on behavior and IQ. There is overwhelming evidence that many traits are heritable, but we lack a genetic theory to explain it.
To believe in counterfactuals, you have to believe that all possible events can be divided into the real and the fictitious. And that you can analyze them as if they had an objective existence. I have this belief because it seems essential to scientific thinking.
We should not accept a concept 100% just because it is convenient for science. Reductionism is convenient for science, but there may be limits to it. Maybe some counterfactuals do not make any sense. So there may be limits to counterfactual reasoning, but it is hard to imagine science without it.