I was messing around with site permissions and wanted to share what I found. In my scenario, I had given a co-worker read access to one of my document libraries, but not my entire site. When I went back in to the site to view the site permissions here is what I saw:
When you click this link, another screen opens and shows you what lists have had unique permissions applied.
The other feature I found helpful, was the Check Permissions option. When you select this you are able to enter a username and it will display for you if that user has been added directly to the site or if they have been placed in a group.
Here is one for a user that was added directly to an item:
This small improvement will be great for troubleshooting access issues!