Directories on ext4 file systems generally have at least 2 links. The entry in their parent directory and the . entry in themselves. See there for more details.
Having said that, if the file system is inconsistent, you may very well have a directory linked in more than one place and the link count not to reflect it.
For instance, with debugfs -w (on an unmounted fs), you can do link a/b c/d to force the creation of a link to a directory. You'll notice that the link count is not updated (you'd need sif a/b links_count 3 to update it):
$ ls -lid a/b c/d a/b/. c/d/.
12 drwxr-xr-x 2 chazelas chazelas 1024 May 14 08:37 a/b/
12 drwxr-xr-x 2 chazelas chazelas 1024 May 14 08:37 a/b/./
12 drwxr-xr-x 2 chazelas chazelas 1024 May 14 08:37 c/d/
12 drwxr-xr-x 2 chazelas chazelas 1024 May 14 08:37 c/d/./
The link count is 2 above, even though there are 3 links (to a, to c, and the "." to itself).
Note that fsck would report a problem with that:
Pass 2: Checking directory structure
Entry 'd' in /c (1282) is a link to directory /a/b (12).
Clear<y>?
So it's unlikely to be your case here if the fs has just gone through a fsck.
To remove one of those links, you can use debugfs -w again (after having unmounted the filesystem) and do unlink c/d in it, or use fsck. If a directory has more than one link, you can check the .. entry within it (with debugfs ls) to check which is the correct one (.. will have the same inode number as its correct parent).
