Backstory...
We have a SharePoint site with some specific permissions set up for various libraries and lists and other groups where we have removed some functions such as the ability to delete.
This morning, I got a message from a manager wondering why they are receiving access requests. I checked the permissions and this is what I found:

I can see that the manager has been given full access through the Owners group yet when I check the Owners permission group, he's not there. Anyone have any ideas? On a separate, yet somewhat related issue, I just received an access request from the site owner. It seems he has no access though he is a site owner.
Any help would be appreciated. Thanks