If I look at the site permissions of a site I can see that some people have both Full Control and Limited Access. The two seem to contradict each other. How can someone have Full Control yet also have Limited Access?
It's just how SharePoint displays permissions. It means that the user has permissions to an object with custom permissions. At the same time, the user is a member of a site group or possesses individual permissions that provide full control permissions. SharePoint will provide the user with the least-restrictive permission set available for that object.
Just because a user has Full Control permissions does not guarantee blanket access. Only Site Collection Admin has that. Full Control users and groups can still be subject to actions that result in the Limited Access designation.
Limited Access means a SharePoint user or group has permissions to an item or document or page or library within a Site, but does not have permissions to the entire Site.
This is normally used when you want to share content that resides within a site with users but not allow to browse the site.
See the following Microsoft TechNet article for further help on the subject.