Following the emergence of 2D materials, a huge amount of work has been dedicated to this new class of materials. Numerical simulations have proven to be powerful to analyze and predict structure-properties relationships. However, a recurrent issue that arises in some 2D compounds is the appearance of a dynamical instability as an unstable phonon branch in a small pocket close the Brillouin zone center. The origin (numerical and/or physical) of this instability is hardly discussed. Here, using a rising 2D material, GaSe, as a case study, this issue is tackled by discussing the numerical techniques that may be used to lift the instability but also by understanding the fundamental origin of it. The interlayer distance is the crucial parameter and the ionicity of the compounds is the key physical property governing the propensity for instability. In many works, this distance is arbitrarily fixed to a value for which the absence of interactions between the periodic images of the layers is assumed. A careful control of the effect of this distance on the stability is required prior to subsequent calculations of physical properties.