We present significant differences in the simulated atmospheric flow for warm, tidally locked small Neptunes and super Earths (based on a nominal GJ 1214b) when solving the simplified, and commonly used, primitive dynamical equations or the full Navier-Stokes equations. The dominant prograde, superrotating zonal jet is markedly different between the simulations, which are performed using practically identical numerical setups, within the same model. The differences arise due to the breakdown of the so-called “shallow-fluid” and traditional approximations, which worsens when rotation rates are slowed, and day-night temperature contrasts are increased. The changes in the zonal advection between simulations solving the full and simplified equations, give rise to significant differences in the atmospheric redistribution of heat, altering the position of the hottest part of the atmosphere and temperature contrast between the daysides and nightsides. The implications for the atmospheric chemistry, and therefore, observations need to be studied with a model including a more detailed treatment of the radiative transfer and chemistry. Small Neptunes and super Earths are extremely abundant and important, potentially bridging the structural properties (mass, radius, and composition) of terrestrial and gas giant planets. Our results indicate care is required when interpreting the output of models solving the primitive equations of motion for such planets.