In this paper we show that BF topological superconductors (insulators) exibit phase transitions between different topologically ordered phases characterized by different ground-state degeneracy on manifold with non-trivial topology. These phase transitions are induced by the condensation of (or lack of) topological defects. We concentrate on the (2+1)-dimensional case where the BF model reduces to a mixed Chern-Simons term and we show that the superconducting phase has a ground-state degeneracy k and not k(2). When the symmetry is U(1) x U(1), namely when both gauge fields are compact, the mixed Chern-Simons model is not equivalent to the sum of two Chern-Simons terms with opposite chirality (even if naively diagonalizable) since the U(1) symmetry requires an ultraviolet regularization that makes the diagonalization impossible. We analyze this aspect using a lattice regularization, where the gauge fields become angular variables. In addition, we will show that the phase in which both gauge fields are compact is not allowed dynamically. Copyright (C) EPLA, 2010