I have only flown into the USA in a widebody a few times.
Once an Aircraft enters the ramp (Termial 2 in this case) the aircraft will switch to RAMP Control (131.375), They are No longer talking to ground control. The aircraft is in the Judistriction of Ramp control, not JFK Ground Control.
It would seem to me that this RAMP Control is a source of problems and lack of coordination at US airfields leading to such accidents.
If both were on the same freq then there would have been a chance that the RJ would have told ground that he was not on stand and ground could have stopped the AF.
It would appear that there are many human factors issues here. The holes in the cheese lined up..........