The basics of the FAA's ATC computer system is that it's used to aircraft being on recognised routes, reflected in the computer 'brain'. When an aircraft flies a direct route, i.e. made up of point to point/non airway routeings, this can cause processing problems unless input correctly. The problem was therefore caused by incorrect input, not the 'spy plane' actually 'frying' anything.
Once again another piece of poor journalism, and actually not worth placing on here...in the nicest possible way! The fact that the jet was at FL600 in LA Centre's airspace meant it was probably a Beale-based bird, which you would've already spotted has been poorly researched in the same article (he mentioned Edwards and what was NASA Dryden, despite actually being the same place, and made no mention of the L-M U-2 'depot' at Palmdale, which is ten yards from the LA ARTCC's front door!).