In some cases the Dashboards Site Health Status will display that your project was not analyzed completely. This can be due to several causes.
Is the URL limit sufficient for my project?
In the project settings you can define how may URLs should be analyzed. If your project contains more URLs than the limit then the analysis will stop once it reached the limit.
Are there settings that may prevent a complete analysis?
A common cause for a incomplete analysis is when obey robots.txt is activated, all 'disallowed' areas from the robots.txt rules will be ignored.
If the option analyze images is deactivated the project will not be analyzed completely if it contains images.
Further causes can come from excluded URLs, you'll find more information here.