Crawl not running according to scope

I ran a crawl with the Custom Page Prefix set to https://med.stanford.edu/whsdm.html and Extra URL Prefixes set to https://med.stanford.edu/whsdm/ and https://med.stanford.edu/content/sm/whsdm/.

However, I noticed that many out-of-scope pages were included in the crawl, such as https://med.stanford.edu/profiles and https://med.stanford.edu/health-care.html.

Any idea what might have gone wrong?