Here's an interesting one, I'm reviewing an issue where the site owners (of a sub-site) cannot access the 'site permissions' page (/_layouts/15/user.aspx). When they try they get a access denied message.
I'm unsure of the history of the site and how this occurred. I have noticed that the groups visible in this sub-site might have been created manually (after he site was provisioned).
In the top level, where it says 'users with limited access', it displays a list of groups of other subsites. There is no group listed for the site with the issue. How can this be rectified? As the sub-site has an owner group, associated with lists/libaries, I did not want to create a new group and re-associate with these lists/libaries :)