Social only has access to count hashtag posts, or mentions of a hashtag rule, on Instagram if it is part of the actual parent post.
If the hash tag Listening Rule is used in an Instagram comment, it is not counted as a mention in Social
The difference between Social counting mentions of # rules on original Instagram posts but not counting them in comments is due to Instagram API limitations.
To troubleshoot concerns about Social not displaying all mentions of an Instagram # Listening Rule, check the native Instagram post. Most likely, the hash tag rules are included in comments and are not part of the initial post.
The Instagram API is a public API. Therefore, Social receives no official support from Instagram if a post is not pulled into Social which should be.