Passively mode-locked lasers with semiconductor saturable absorption mirrors are attractive comb sources due to their simplicity, excellent self-starting properties, and their environmental robustness. These lasers, however, can have an increased noise level and wake mode instabilities. Here, we investigate the wake mode dynamics in detail using a combination of evolutionary and dynamical methods. We describe the mode-locked pulse generation from noise when a stable pulse exists and the evolution of the wake mode instability when no stable pulse exists. We then calculate the dynamical spectrum of the mode-locked pulse, and we show that it has six discrete eigenmodes, two of which correspond to wake modes. The wake modes are unstable when the wake mode eigenvalues have a positive real part. We also show that even when the laser is stable, the wake modes lead to experimentally observed sidebands.