Ray tracing techniques have been used to investigate numerical effects on the propagation of acoustic waves in a non-hydrostatic dynamical core discretised using an Arakawa C-grid horizontal staggering of variables (Arakawa & Lamb 1977) and a Charney-Phillips vertical staggering of variables (Charney & Phillips 1953) with a semi-implicit timestepping scheme. It is found that the space discretisation places limits on resolvable wavenumbers and redirects the group velocity of waves towards the vertical. Wave amplitudes grow exponentially with height due to the decrease in the background density, which can cause instabilities in whole-atmosphere models. However, the inclusion of molecular viscosity and diffusion acts to damp the exponential growth of waves above about 150 km. This study aims to demonstrate the extent to which numerical wave propagation causes instabilities at high altitudes in atmosphere models, and how processes that damp the waves can improve these model’s stability.