The non equilibrium Green function formalism is today the standard computational method for describing elastic transport in molecular devices. This can be extended to include inelastic scattering by the so called self-consistent Born approximation (SCBA), where the interaction of the electrons with the vibrations of the molecule is assumed to be weak and it is treated perturbatively. The validity of such an assumption and therefore of the SCBA is difficult to establish with certainty. In this work we explore the limitations of the SCBA by using a simple tight-binding model with the electron-phonon coupling strength α chosen as a free parameter. As model devices we consider Au mono-atomic chains and a H2 molecule sandwiched between Pt electrodes. In both cases our self-consistent calculations demonstrate a breakdown of the SCBA for large α and we identify a weak and strong coupling regime. For weak coupling our SCBA results compare closely with those obtained with exact scattering theory. However in the strong coupling regime large deviations are found. In particular we demonstrate that there is a critical coupling strength, characteristic of the materials system, beyond which multiple self-consistent solutions can be found depending on the initial conditions in the simulation. We attribute these features to the breakdown of the perturbative expansion leading to the SCBA.

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