Another thing that can be difficult for filleting is tight bends in the thing being filleted. You've got quite tight bends in both tip areas of that scooped out part, and it looks like the filleter is getting confused when trying to negotiate the tight bend in the top piece and the thing it generates does not quite hug the object right in that corner area, which is why it's having problems trying to trim the object with the fillet outline.

It's kind of 2 things there actually - a tight bend in the shape being filleted and also near the top the scalloped out part approaches fairly close to being tangent to the dome piece, that also tends to confuse the filleter because fillets start to kind of disappear to zero area in places where 2 surfaces are smooth to one another.

- Michael