The hypotheses about reasons for the inverse dependence of the turnover frequency of hydrogenation of unsaturated compounds (alkyne, alkynol, olefin) on the catalyst concentration were discriminated by kinetic methods combined with electron microscopy. The reasons are: dissociation of polycrystalline Pd–P particles, equilibrium shift (stabilized cluster–cluster + stabilizer), and aggregation–disaggregation of Pd–P particles, the latter being the main reason for the concentration range 0.125–1 mmol/L. The effect of aggregation–disaggregation of Pd–P particles on the catalyst activity differs depending on the substrate. The proposed kinetic model was shown to be consistent with the experimental data for styrene hydrogenation used as an example. The rate constants of some stages were determined.