Problem:  unable to delete SharePoint Online site/site collection due to permissions even though account being used is in the owner permissions group.

Solution:  ​OK… so with a little help on the backend from MS support I was able to fix the issue with permissions on an internal team site and successfully delete the unwanted site.

By going to: https://TENANTNAME.sharepoint.com/SITENAME/_layouts/15/deleteweb.aspx

(Replace both TenantName and SiteName with specific values)

You can Delete the Website.  The problem in this case was the migration from Wave 14 to Wave 15 when a team site was created before the migration on the backend.  Also noted was the change in the tenant logon ID changing to different values.  This cause an odd problem where owner permissions were hosed.

*NOTE:  do not delete the Search teamsite!