Seems that the comment count gets mixed up sometimes by this and other plugins.
Found a nice Fix that worked fine for here:
https://bit.ly/1ra0V2O
Nevertheless you should fix this in your plugin.
Here the code of the post slightly modified by me since it was tied to a specific database name:
/* Query for checking before and after fixing posts/pages with wrong count */
SELECT wpp.id, wpp.post_title, wpp.comment_count, wpc.cnt
FROM wp_posts wpp
LEFT JOIN
(SELECT comment_post_id AS c_post_id, count(*) AS cnt FROM wp_comments
WHERE comment_approved = 1 GROUP BY comment_post_id) wpc
ON wpp.id=wpc.c_post_id
WHERE wpp.post_type IN (‘post’, ‘page’)
AND (wpp.comment_count!=wpc.cnt OR (wpp.comment_count != 0 AND wpc.cnt IS NULL));
/* Query for actually fixing the count for all affected posts */
UPDATE wp_posts wpp
LEFT JOIN
(SELECT comment_post_id AS c_post_id, count(*) AS cnt FROM wp_comments
WHERE comment_approved = 1 GROUP BY comment_post_id) wpc
ON wpp.id=wpc.c_post_id
SET wpp.comment_count=wpc.cnt
WHERE wpp.post_type IN (‘post’, ‘page’)
AND (wpp.comment_count!=wpc.cnt OR (wpp.comment_count != 0 AND wpc.cnt IS NULL));
