Oh okay, that is different.
The number of items shown there is requested from the WordPress core itself via the get_term_by function, it is not the plugin querying it, it only prints the count reported by WordPress itself.
From what I know, this number is heavily cached for performance reasons. It is possible that you may have to update or visit the category page on the back-end to update it. If the number is still incorrect, then something else must be changing it – either a 3rd party code or a plugin via a custom code, but it should always report the correct count.