Listening to the tapes over at liveatc.net, United 211, a B-739 YYZ-ORD was cleared for takeoff on 06L. Envoy 3725, an ERJ-145 JFK-YYZ after landing on 06R was cleared to exit at D3, hold short of 06L.
A tower voice shouted for Envoy to 'Stop!' and, a little later after the RJ was cleared across 06L, asked if he saw the stop bar.
While taxiing in Envoy was given a phone number to call and the outbound sector back to JFK was cancelled.