A drug substance intermediate synthesis involving a Mitsunobu coupling reaction using triphenylphosphine and diisopropyl azodicarboxylate was investigated to understand the variable levels of an impurity. One of the precursors for the impurity, 1,2-isopropylhydrazine dicarboxylate (a reaction byproduct), crystallizes out of the reaction medium and also forms a cocrystal with triphenylphosphine oxide (TPPO), another reaction byproduct. The dynamic byproduct concentrations as a result of these phenomena were taken into account in a reaction kinetics model. The variability in impurity formation was linked to the concentration of 1,2-isopropylhydrazine dicarboxylate, which is dependent on reaction progress and 1,2-isopropylhydrazine dicarboxylate-TPPO cocrystal formation. The cocrystal formation is in turn affected by the mixing characteristics in the reactor. Computational fluid dynamics simulation of the mixing patterns and a series of proof-of-concept experiments were performed to establish the influence of mixing intensity and cocrystal formation on the level of impurity formed.