There are two main reasons why you see that Site Audit has only crawled a few pages on your project. 

If you used the "www" version, but your main site is non-www, Site Audit will be unable to crawl your site.
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The easiest way to check what the site is like is to open that site in a browser:

If the "www" part is not there, you should not include when starting your audit. 

If your site is JS-powered, you need to enable the Execute JavaScript option when setting up your crawl:

This should resolve the issue with the number of pages crawled.