A large number of studies of mixed-matrix membranes (MMMs) have confirmed the possibility of obtaining new materials with unique transport properties, including for solving specific problems in the separation of mixtures of liquids and gases. The choice of particles with a given affinity for the matrix and separable components allows researchers to adjust the selective properties of MMMs in a wide range, which changes the properties of MMMs in a wide range. However, even within the framework of the most complex percolation mechanism of the formation of the MMM structure, it is possible to explain only some of the observed effects. In particular, questions about the required particle concentration and fluctuation of properties in various MMM samples are still the subject of research. The results of the numerical modeling of such structures presented in this paper determined the possible causes of the observed deviations of the experimental results, for example, particle size dispersion, agglomeration, and interaction with the matrix. According to our research, the key factor that qualitatively changes the parameters of percolation structures is the ratio of the geometric dimensions of the system. We have confirmed in a wide range a significant change in the conditions of cluster formation and its power at different particle diameters and lengths (traditional parameters in percolation studies). But in our work, we additionally studied the effect on the cluster parameters of the interfacial layer and the anisotropy of the matrix (the transition from the cube to the film). The results obtained show that changing the parameters of the matrix-particle interaction affects agglomeration, and the degradation of the percolation structure is possible. That is, with an increase in concentration, the parameters of the percolation cluster, its power, and the probability of formation, may decrease. But even more negative changes in percolation structures are observed during the transition from a volumetric matrix to films. The anisotropy of space leads to the formation of percolation through the film in certain areas at low concentrations of particles. At the same time, in a significant part of the matrix, percolation between the film surfaces will be absent, and the effect of changing the properties of MMMs in the matrix as a whole decreases. Our study explains the observed instability of MMM properties at fixed concentrations and parameters of embedded particles, including the effect of reducing the influence of particles with increasing concentration.