NTFS Permissions On Windows Server 2003

I have a server running windows server 2003 with an active directory. I have subcontainers in the active directory holding users accounts that belong to diffrent groups, these groups then have logon scripts assigned to them to map certain folders to drives when the user logs on. These folders then have NTFS file permissions on them only allowing certain groups to access them. I have tested the permissions on all of these folders many times using diffrent accounts and have found no problem, However some of the users like to ‘mess around’ with the files on the network and have got into folders they do not have access to.
Please Help I Have Struggled For Ages On This And Feel Like Someone How Doesn’t Know Anything Anymore !!!!!