I have a document library with item level permissions set for the documents. Users with contributor access for a document cannot check a document into the library. Access Denied error comes up before the check in screen is displayed. If I give the user read access to the library, they can check in. Is there a way to give a user permission to check a document into a library without having read permission on the entire library?
As commented by Robert... first check if there is any workflow or feature attached with the document library that might be altering the user permissions.
The user must have at least read permission to the document library in order to access it. The item level permission may differ. Example... the user can have contribute permission only on 50% of the documents in the library.
To check-in a document the user must have Contribute permission or any custom level permission that allows the users to check-in the document. Having only read permissions will not allow users to check-in a document.
You don't need to give read permissions to the entire library, just to this item. IMHO is to verify the permissions one more time.
You can find the permissions levels at http://technet.microsoft.com/en-us/library/cc721640(v=office.15).aspx
Also check, in list settings/versioning settings/ who can see an item.