The 1998 championship was to prove controversial for Loughnane and his Clare team. The replayed Munster final against Waterford was played in an extremely poor spirit with Colin Lynch of Clare and Michael White of Waterford being sent-off after a huge melee. Lynch received a three-month ban for his part in the game and Loughnane was disgusted at the decision. In spite of that Clare captured a third Munster title in four years. The subsequent All-Ireland semi-final saw Clare draw with Offaly. More controversy was to follow when Clare played Offaly in the semi-final replay. Clare were winning by two points when the referee, Jimmy Cooney, blew the whistle with two minutes of normal time left to be played. The Offaly fans were outraged and staged a sit-down protest on the pitch. The result wasn't allowed to stand and Clare were forced to meet Offaly for a third time that year. They lost the second replay, however, it has been said that if they won they would have captured a second All-Ireland title in-a-row. 1998 marked the end of the success for Loughnane's Clare side.