With more extensive testing i found a issue which is too rare. If a request is made during update between user meta delete and message update (time is less than 1 second depending on your messages size) then this issue occur. I believe which is case for you.

You can add delete_metadata( 'user', 0, '_fep_user_message_count', '', true ); in your theme’s (child theme’s if any) functions.php, then refresh your admin area couple of times and remove this code. This will solve your issue.