Ive got an issue with Smart Crawl showing 3 different resuts

So on wpmudev, ive got a -96 score and warning that my main site lucidhive.com is not listed in my site map.

Runnning the test in WP dashboard its showing 0 issues finally after 2 months of not working.

Then on google once re crawling the site I have 159 items of "404s" which I would like to change and thought I didi when changeing the settings on what to index.

PLease Help!!