That's not the problem of the concept of an index. It's bad implementation. If your index only indexes as if it were a static folder structure, then you have to think exactly like the guy that built the index. If you instead allow multiple indexes/index entries for the same underlying thing, then you have tagging.

Bookmarks are folder structure. Theoretically you can bookmark the same thing under a different part of the structure of course. I've never really seen people do that though, except accidentally because they found something the liked, bookmarked it in on place, later found it again, didn't remember they already bookmarked it and bookmarked it in a different part of their folder structure. In a way they also "tagged" except that the actual bookmark, the thing is not the same. It's a copy. If your bookmark goes to some address that might change while pointing to the same actual thing, you'd now have to update (and first find) a multitude of bookmarks in your folder structure. A file system that has hardlinks could implement "tagging" too :)