Fills work using the boundaries of the shape to toggle the fill on and off, as shown in the full-screen image below. This is expected and useful behavior, not an error. While not producing as you would like, this is not an error condition.
You can use the ‘Edit’→’Delete Duplicates’ to help identify and remove unwanted duplicates when you experience these issues. In most cases, the duplicate is visible as darker than other shapes, and the marquee when selected can be obscured by the duplicate.
(Example: In this view, two of the 3 shapes are selected)