An audit can finish with fewer pages than you asked for. The usual reasons, most common first:
You asked for more pages than the site has
If you set 1,000 pages and the site has 300, the audit stops at 300. That is a complete audit, not a truncated one.
You reached your monthly crawl cap
Every plan includes a set number of audit pages per month (why it works this way). At the cap, audits pause until the reset. Site Health shows how much you have used.
Pages are not linked from anywhere
The crawler follows links, the same way a search engine does. A page nothing links to will not be found unless it is in your sitemap — and that is worth knowing in itself, because search engines have the same problem with it. Those pages show as Not linked in the results.
The site blocked the crawler
Some firewalls and security plugins block anything that is not a person browsing. When that happens the audit reports the pages as blocked rather than pretending they are fine. Allowing our crawler in your firewall fixes it — the results screen shows the exact rule to add.
The audit failed partway
If something goes wrong mid-crawl, we keep the pages already crawled and show the report rather than discarding the work. The run is marked so you know it is incomplete.
Re-running usually just works. If it keeps stopping at the same point, contact support with the audit link and we will look at the log.