We determine the phase diagram and pion spectrum for Wilson and twisted-mass fermions in the presence of nondegeneracy between the up and down quarks and discretization errors, using Wilson and twisted-mass chiral perturbation theory. We find that the CP-violating phase of the continuum theory (which occurs for sufficiently large nondegeneracy) is continuously connected to the Aoki phase of the lattice theory with degenerate quarks. We show that discretization effects can, in some cases, push simulations with physical masses closer to either the CP-violating phase or another phase not present in the continuum, so that at sufficiently large lattice spacings physical-point simulations could lie in one of these phases.