There are two main reasons why you see that Site Audit has only crawled a few pages on your project.
1. You used the "www" version
If you used the "www" version, but your main site is non-www, Site Audit will be unable to crawl your site.
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.
This should resolve the issue with the number of pages crawled.