Unable to add color to certain region of shapes

first, there are a paint bucket fill options that automatically close gaps:

that will probably help you avoid problems.

but to see small gaps, use the zoom tool to drag a rectangle around the shape (or parts of the shape):

before zoom:

after dragging zoom tool magnifier:

now, this shape may look like it's closed, but it is not.  ie, it won't fill unless you select the close medium (or large gaps) option which surprised me.  i thought selecting close small gaps would be sufficient.