Category links appear in the side filter even when the flags "Category appears in the top menu and side menu of the Site" and "Category has an active link on the Site" are disabled.

1. Access the catalog.
2. Acess Categories.
3. Select a category.
4. Click Actions > Change.
5. Deselect the flags "Category appears in the top menu and side menu of the Site" and "Category has an active link on the Site".
6. Enter the category page one level above through the store.

To hide these unwanted categories on the front-end, the workaround would be to implement a script that hides the H4 tags that don't have an A tag as their child.