The appearance of your sitemap is not based on which folders within your webserver that your pages are stored, as this may not necessarily reflect the layout / flow of your site.

Rather, your sitemap is built based on the design / flow of your site as one page links to another.

Therefore, as the FusionBot spider begins indexing your site, starting with the default / start page provided, the first time a link to a particular page is found on your site, this page is added to the indexing queue.

Thus, all links found to additional pages from your default page are denoted on your sitemap as a second level, one below your default / startpage.

Anytime a link to the same page is found elsewhere, this link is ignored, as it has already been indexed and found at a higher level, taking precedence over any other link.

As the spider then begins indexing your second level of pages, all new links found at this level will now become the third level of links on your sitemap and so on.

Each time a new level of indexing begins, all links from this level are first added to the queue, under the corresponding page in which the new link was found first. This is why your sitemap will continue to build to the right as the indexing progresses.

Therefore, if a second level and a third level page both link to the same page, the linked page will appear as a child of the second level page, rather than below the third level.

The appearance of your sitemap is a direct reflection of the order in which the links to additional pages on your site are found, and their depth as they are linked from one page to another.

If your site has multiple links to the same page, and you do not wish for a particular link to appear as a sub-page of the location where it is currently located, you can go to the current location / page and add a custom FusionBot tag, instructing the spider to ignore this link in favor of the same link found elsewhere on your site, likely at the location where you wish for the page to appear within your sitemap.

Following is a link to our FAQ on the <nofollow> custom tag to address this problem:

Skip indexing specific links