RWY INCURSION CREATES A GND CONFLICT BTWN A C650 ON THE RWY AND AN APCHING B757 AT JFK; NY.

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WORKING LCL CTL; LNDG AND DEPARTING RWYS 31L AND 31R. I INSTRUCTED AN SF340 (Z) TO TAXI INTO POS AND HOLD RWY 31R. THERE WAS A BUZZ ON THE FREQ; THEN THE SF340 FLC CLRLY READING BACK HIS CALL SIGN AND 'POS AND HOLD; RWY 31R.' SUBSEQUENTLY I SAW A C650 (X) IN POS ON RWY 31L WITH TFC; A B757 (Y) ABOUT 1 MI OUT. I INSTRUCTED THE C650 (X) TO EXIT THE RWY TO THE L AND THE B757 (Y) LANDED. CONTRIBUTING FACTORS: PRIOR TO THE INCIDENT 4 ACFT; INCLUDING THE C650; CALLED FOR PERMISSION TO CROSS AN INTERSECTING INACTIVE RWY AFTER THEY HAD ALREADY BEEN CLRED TO CROSS BY GND CTL. THIS ADDED TO THE CONGESTION AND COMPLEXITY ON THE FREQ. IT ALSO ILLUSTRATES THE LACK OF ATTN BEING PAID TO CTL INSTRUCTIONS. OTHER INSTRUCTIONS ON MY FREQ INDICATED THAT THE B757 (Y) TFC WOULD LAND RWY 31L PRIOR TO THE C650'S (X) DEP. I FEEL MORE ATTN SHOULD BE PAID TO ALL XMISSIONS ON A FREQ; NOT JUST THE ONES DIRECTED TO A PARTICULAR ACFT; THEREBY INCREASING SITUATIONAL AWARENESS. THIS INCIDENT ALSO ILLUSTRATES THE OVER-EMPHASIS ON QUICK DEPS BY SOME ACR'S AND THEIR HABIT OF HEARING WHAT THEY WANT TO HEAR; NOT WHAT WAS ACTUALLY SAID. SUPPLEMENTAL INFO FROM ACN 564988: THE ACFT WAS READY TO DEPART ON RWY 31L AT JFK INTL WHEN THE CREW THOUGHT THAT THEY WERE CLRED INTO POS AND HOLD ON THAT RWY. THE CTLR WAS WORKING BOTH RWYS 31L AND 31R AND HAD CLRED ANOTHER ACFT INTO POS AND HOLD ON RWY 31R. WE ACCEPTED THE CLRNC AND TAXIED INTO POS ON RWY 31L. ABOUT 1 MIN LATER THE TWR CAME ON AND INSTRUCTED US TO EXIT THE RWY TO THE L IMMEDIATELY DUE TO AN ACFT ON FINAL. ONCE CLR I RPTED TO THE TWR THAT I WAS CLR OF THE RWY. THIS INCURSION HAPPENED DUE TO A COM ERROR BTWN THE CREW AND THE CTLR. THE CTLR TOLD ANOTHER ACFT THAT WAS #2 FOR LNDG THAT THERE WOULD BE A DEP PRIOR TO THEIR ARR. THIS MAY HAVE GIVEN THE CREW THE THOUGHT THAT THEY WERE GOING OUT SOON AND MISINTERPRETED THE POS AND HOLD CALL TO BE THEIRS. THIS COULD BE AVOIDED IF WHEN USING MULTIPLE RWYS THAT THEY USE MULTIPLE FREQS; EVEN THOUGH TFC MAY BE LIGHT. I WOULD ALSO STATE THAT; IF THERE WERE SOME RADIO INTERFERENCE DURING A READBACK THAT THE CTLR RESTATE THE INTENDED COM TO ALL ACFT AND ESPECIALLY WHEN THE CTLR IS WORKING MORE THAN 1 RWY.