CE560 LNDG HWD CROSSED PARALLEL RWY AFTER BEING INSTRUCTED TO HOLD SHORT.

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WE LANDED ON RWY 28L AT HWD AND STARTED TO CLR AT TXWY D. THE TWR ADVISED US TO TURN R AT TXWY E. WE CONTINUED DOWN THE RWY AND TURNED N AT TXWY E AND CONTINUED ONTO RWY 28R TOWARDS THE PARKING AREA. I CHKED L AND HEARD 'OH @&*$' ON THE RADIO AND LOOKED R TO SEE AN ACFT CLBING OFF RWY 28R. THE CLBING ACFT APPEARED TO BE APPROX 200-300 FT AGL; AS IT WENT OVER TOP OF US. TWR ADVISED THAT WE HAD BEEN TOLD TO HOLD SHORT OF RWY 28R! CONTRIBUTING FACTORS MAY HAVE BEEN THE FACT THAT WE HAD BEEN HAVING TROUBLE WITH INTERCOM COM IN THE COCKPIT WITH THE CAPT'S SIDE HEARING BROKEN RECEPTION FROM THE COPLT'S SIDE. ON AT LEAST 5 OCCASIONS; I STATED THAT I WAS ONLY HEARING EVERY SECOND WORD AND ASKED THE COPLT TO PLACE THE MIKE CLOSER TO HIS MOUTH. (WE EVEN SWITCHED TO A SPARE HEADSET EARLIER IN THE FLT; TO TRY AND ALLEVIATE THE SITUATION.) THE COPLT CLAIMS HE HEARD THE CTLR'S INSTRUCTIONS TO HOLD SHORT OF RWY 28R. I DID NOT. NOR DID I HEAR THE COPLT REPEAT THAT INSTRUCTION. THE COPLT SAID HE HAD GONE 'HEADS DOWN' AS WE TURNED THE CORNER ONTO TXWY E AND HE DID NOT LOOK R PRIOR TO ENTERING THE RWY; OR NOTICE THAT WE WERE ACTUALLY XING RWY 28R; UNTIL HE HEARD THE RADIO EXCLAMATION AND LOOKED UP. THIS IS A CLASSIC CASE THAT PROVES; ONCE AGAIN; NO MATTER HOW EXPERIENCED (36 YRS IN MY CASE) WE ARE ALL HUMAN AND ERRORS CAN AND DO OCCUR. FOR 7 YRS I HAVE BEEN HEARING; 'TURN R; TAXI TO PARKING' 99.9% OF THE TIME; AT THIS ARPT AND I MAY HAVE BEEN PROGRAMMED TO DO JUST THAT. I AM GRATEFUL THAT NO ACCIDENT RESULTED AND THAT WE CAN ALL GO HOME TO OUR FAMILIES. REST ASSURED; I WILL BE EXTREMELY VIGILANT WHEN APCHING OR XING ANY RWY FOR THE REST OF MY CAREER! I PAID A VISIT TO THE TWR AFTERWARDS AND FOUND THAT THEY WERE SHORT-STAFFED WITH A NEW TRAINEE AND ONLY 1 PERSON CHKED OUT ON 'GND.' WOULD THEY HAVE NOTICED THAT WE WERE NOT STOPPING; OTHERWISE? WE WILL NEVER KNOW AND YOU SHOULD NEVER COUNT ON IT! PLEASE FLY SAFE AND TAXI SAFE; TOO!