One of my co-workers had an issue with SPO where a user she added to the owners group still had no permissions on the site.
We opened a case with Microsoft and the issue was some weird permissions issue : the Site owners group didn’t have the correct permissions to grant or modify permissions for users or to view the related settings pages in site settings. Microsoft said it was related to the access request list.
MS provided a KB article: https://support.microsoft.com/en-us/kb/2911390
My Super-Awesome-Fantastic Co-Worker Melissa Seals did all the work on this case, so I can’t claim to have any part in the solution, but it seemed obscure enough that it’s worth documenting here should we ever need it again. (She followed the steps in the article and got it working!)