SEO Checkup in subsite scanning the main site

I have a subdomain multisite installation with mapped domains. I have SmartCrawl network enabled. When I run a SmartCrawl Checkup in a domain mapped subsite, it scans the main site for SEO issues and not the subsite where the checkup is ran from. FYI, the “Sitewide Mode (Network Level Changes Only)” option is disabled in the SmartCrawl network settings.