This is by design, since there is no way to know if a cropped shape is a closed circle or an open arc.

From the API documentation of binary_fill_holes

Notes

The algorithm used in this function consists in invading the complementary of the shapes in input from the outer boundary of the image, using binary dilations. Holes are not connected to the boundary and are therefore not invaded. The result is the complementary subset of the invaded region.

Here's two examples of what the rest of the shape could be