Neutrino conversions in supernova may freeze or diverge for certain parameters. In some rare cases the MSW routine may miss or mishandle a resonance - occurs mostly for complicated 4 flavour supernova simulations, resulting in weird neutrino spectra. If you do not have three massive neutrinos an exception will occur. Atmospheric neutrino model very poor - the code has been calibrated with some artificial parameters. Checks for many laboratory constraints not done yet.
Astrophysical constraints are rather crude.
Phenomena in the core of supernovae not yet studied. Also other supernova code is very primitive. Early universe not simulated either. No links to references. Feedback effects in neutrino conversions ignored.