Naughty Sphere's

 From:  Lemo (LEMONNADO)
I am running constantly into problems with spheres. When I 'bool' a dent into a sphere with another smaller sphere, then I can fillet the rim nicely as long as it does not intersect with the 'seam'. The moment that seam on the sphere is involved many functions just don't work right. How can I avoid the trouble with those naughty spheres?