The physical contents of a file (inode, or ino) normally has one link to it, the directory entry for the file name. If multiple names have been linked to the same physical contents via a hard link (see "man ln") there will be an additional link for each additional name. You can use "ls -l" to see the number of links for each file in a directory. Each directory normally has two links to it, the directory itself and the parent directory. The messages are telling you that the link counts in the inodes themselves are different than the number of links found to the inode.
