Murphy has clashed with Stephen Maguire, another of the 2000 Young Players of Distinction, on several occasions. At the start of their 2004 Grand Prix match, there was an incident that resulted in Maguire being docked the opening frame. After they had shaken hands at the outset of the first frame, Maguire asked referee Johan Oomen for permission to leave the arena and retrieve his chalk, which he had forgotten. While Maguire was away, the referee and Murphy spoke before tournament director Mike Ganley arrived on the scene and docked Maguire a frame for technically not being ready to start at the scheduled time, which angered and surprised Maguire. Murphy refutes that the docking of the frame was down to him speaking to the referee. Maguire won the match 5–2 and later commented: "Rules are rules but I've never heard of anything like that happening before".
