During the last 15 years, methods for the capillary electrophoretic separation of different bacteria species have been developed, which exploit their characteristic cell surface-charge to volume ratio. A special variant, the polymer-based CE of bacteria, includes a focusing step, which forces the bacteria cells to form aggregates at the beginning of the electrophoretic process, resulting in very high apparent efficiencies. Our experiments presented in this article reveal that the migration time of bacteria species in polymer-based CE increases with a growing amount of injected cells. Thus, the electrophoretic mobilities are not characteristic for the single cells of one species, but for the aggregates of the bacteria species, which are formed during the focusing process. Electrophoretic mobility (EM) data are obviously inapplicable for the identification of bacteria if the concentration of the bacteria sample solution is not constant. Fractions taken during the electrophoretic separation of different bacteria species were cultivated and tested for species purity. Interestingly, the electrophoretic bands were never pure, as all of them contained different mixtures of the injected species. We attribute this to the formation of stable mixed-species aggregates during polymer-based focusing. The mixed clusters migrate in the electric field with consistent velocity as a whole and are not separated electrophoretically.