Dark solitons in superfluid Bose gases decay through the snake instability mechanism, unless they are strongly confined. Recent experiments in superfluid Fermi gases have also interpreted soliton decay via this mechanism. However, we show using both an effective field numerical simulation and a perturbative analysis that there is a qualitative difference between soliton decay in the BEC- and BCS-regimes. On the BEC-side of the interaction domain, the characteristic snaking deformations are induced by fluctuations of the amplitude of the order parameter, while on the BCS-side, fluctuations of the phase destroy the soliton core through the formation of local Josephson currents. The latter mechanism is qualitatively different from the snaking instability and this difference should be experimentally detectable.