Stably stratified layers are present in stellar interiors (radiative zones) as well as planetary interiors - recent observations and theoretical studies of the Earth's magnetic field seem to indicate the presence of a thin, stably stratified layer at the top of the liquid outer core. We present direct numerical simulations of this region, which is modelled as an axisymmetric spherical Couette flow for a stably stratified fluid embedded in a dipolar magnetic field. For strong magnetic fields, a super-rotating shear layer, rotating nearly 30% faster than the imposed rotation rate difference between the inner convective dynamo region and the outer boundary, is generated in the stably stratified region. In the Earth context, and contrary to what was previously believed, we show that this super-rotation may extend towards the Earth magnetostrophic regime if the density stratification is sufficiently large. The corresponding differential rotation triggers magnetohydrodynamic instabilities and waves in the stratified region, which feature growth rates comparable to the observed timescale for geomagnetic secular variations and jerks. In the stellar context, we perform a linear analysis which shows that similar instabilities are likely to arise, and we argue that it may play a role in explaining the observed magnetic dichotomy among intermediate-mass stars.