FWIW, fillets give Solidworks trouble too. Never build child geometry on top of fillet parents if you can avoid it because it's likely to blow up on later rebuilds.
True, but this isn't having so much to do with the fillet itself, but with the child geometry referencing outputs of the fillet command like edges and surfaces of the fillet. It you go back later and then change the fillet radius, delete it and add another in its place, etc. Those references get messed up.