In many kinds of Godunov schemes (including Athena), strong planar shocks in multidimensions that propagate along a grid direction can be subject to a numerical instability that causes large amplitude perturbations in the shock front at the grid scale. This is often called the carbuncle instability.
Fixing the carbuncle instability requires adding extra dissipation in the direction perpendicular to the shock only. We have found the best way to do this is using the H-correction, see Appendix C in the ApJS Method Paper for details.
To use the H-correction, use the Roe flux, and enable the correction during configure using:
% configure --with-flux=roe --enable-h-correction
The H-correction is not needed for most problems. It is only required when there are strong planar shocks propagating parallel to grid lines for a significant fraction of a dynamical time.