That's okay, there can be duplicates of object_id (and also duplicates of term_taxonomy_id), but it doesn't matter in this case because the terms themselves are separated into multiple taxonomies. Tags and categories can only attach to posts. link_categories can only attach to links. These are defined with different taxonomies (using the taxonomy column in the term_taxonomy table).
In your given case, term_taxonomy 1 and term_taxonomy 5 have a taxonomy of either "tag" or "category". term_taxonomy 12 has a taxonomy of "link_category".
Also note that because of this, there cannot be duplicates of the primary key, because it includes both the object_id and the term_taxonomy_id, and each term_taxonomy entry falls into only one taxonomy.