I was told about an incident either last night (1/2 or 1/1) at JFK where a Freedom aircraft landed on 22L, taxied right across 22R while an aircraft was its departure roll. The departing aircraft's crew has been removed from duty to debrief the incident.
Freedumb was actually departing 31L, either on the Breezy Point or Canarsie climb. Being a WAVEY departure, I think that puts him a Canarsie climb, if I remember correctly. Not sure if he didn't make the 2nd turn at Canarsie or what.
It sounds as if the pilot blames it on the FMS. Unfortunately, you are still in command of the aircraft and are supposed to make sure it goes where you tell it to. Per our manuals/procedures, my airline is not permitted to use any automation for the Canarsie and Breezy Point climbs. We must navigate by the old style VOR tracking (if the weather is good, I usually make the first turn to CRI visually since I know exactly where the VOR is).