"But no need to used (for avoid any problem) it if you turn the Generator curve of the sphere before the Union! ;)
It must don't touch the cube!
Then Fillets works like a charm! :)
Don't ask me why! :) you must turn it! (fillet 1 will be fine)"

This is an often valid solution indeed. Calculations like fillets are more prone to failure if the fillet crosses a surface seam.