Whether it be a Traffic Collision Avoidance System (TCAS) alert, one or more pilots spotting the potential conflict visually, or even having a "strong gut feeling" that something isn't quite right based on one's situational awareness(1), pilots (at least in the US and most likely worldwide) are authorized by regulations to take any action they deem appropriate to ensure the safe operation of the aircraft, including ignoring or temporarily deviating from an ATC instruction.
(1) - There was a case recently of an airliner here in the States who got lost while taxiing and soon thereafter ATC cleared another aircraft (a USAir jet, IIRC) for takeoff. The pilot of the jet that was cleared to takeoff overrode ATC's instruction and held at the runway because he didn't like what he was hearing from ATC and the lost pilot's communications - come to find out the lost aircraft was actually sitting on the runway about two thirds of the way down and had the second aircraft taken the runway, there most likely would have been a collision.
edit: I apologize but it would take a bit of research to find the reference of this incident, but I suspect other pilots here might recall it.