This is the second time this has happened at JFK, a Saudia 747 clipped a BAE 146 tail, in the early nineties if memory serves.
I'm going to hazard a guess here. The A380 was certainly taxiing down the centerline, and I'm also assuming the CRJ was stopped at his usual spot on the Comair ramp awaiting a marshaller.
JFK is an old airport with narrow taxiways, and incredibly busy around trans-Atlantic departure time. Whoever was responsible for ensuring Taxiway Alpha was suitable for the A380's wingspan, the FAA is my guess, may have dropped the ball on this one.
I'm sure they're already out there with rulers, pencils and measuring tapes, fine-tooth combing for any other spots they've missed.