If you need the Sharepoint Crawler to a exclude a site, you cannot use the absolute path in the Exclude Filter.
Resolution
Let's say you have a site https://my-site/company.com/personal/site1 that you want to exclude, then in the Exclude Filter, you will need to put the following:
/personal/site1/*
/site1/*
Note: There is a 1024 character limit for this exclusion list.