instance_occurrence counts how many times the link text occurs before the point where it should be linked. This is now based on wikitext, which cannot be used for Parsoid HTML. It should be based on plaintext instead.
In other words, when the service suggests changing Scary careening <!-- scared --> car to Scary careening <!-- scared --> [[car]], currently instance_occurrence is (assuming 1-based indexing) 4 but it should be 3 as we want to disregard the comment. Same goes for template parameters etc.