Hello,
Could you please describe what do you mean by ‘missing product in the category’ and ‘variant appearing in category grid.’?
Initially, you were talked about the product gallery. Yes, our theme overrides both files mentioned by YITH reply and, unfortunately, we are not able to implement all our theme features for the product gallery without doing that. So if the plugin does the same from their side or rely on WooCommerce standard functionality then it will not be compatible with our theme gallery. You can remove those files but then you will lose all our theme gallery-related functions and layouts options and get a standard WooCommere gallery.
Kind Regards