In refining processes, such as purification of metals or materials, the system inherently resists order due to the second law of thermodynamics.
Entropy, which is a measure of disorder, tends to increase in natural processes.
When refining is done to make a system more ordered (i.e., reduce impurities), it requires input of energy and effort to reduce entropy.
Thus, the entropy of the system acts in opposition to the refining process, which is why it is said to "work against the refiner".