I think you misunderstand evolution theory. It does not state that the number of species must increase with time. Evolution allows for species to go extinct. Therefore, the number of species can increase,decrease or remain steady with time. It simply depends on whether the rate of speciation or the rate of extinction is higher. Furthermore, there is nothing in evolution theory, per se, that even mentions phyla. It simply states that, over time, the relative frequency of alleles in a given gene pool will change.