Optimize group by sub query in Mysql

IN clause the way you used it would be very slow, use JOIN instead:

SELECT r.* FROM ( 
  SELECT r1.id AS id
  FROM faultrefunds_v2 r1 
  GROUP BY faultid
  HAVING count(r1.faultid) > 1
) AS ids
LEFT JOIN faultrefunds_v2 AS r
ON( ids.id = r.id )