B757 FLC CROSSES HOLD SHORT LINE OF ACTIVE RWY CAUSING ACFT ON APCH TO GAR.

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ON INITIAL CALL UP TO MIA GND CTL; WE WERE ISSUED 'TAXI TO RWY 09L VIA N.' SHORTLY AFTER TURNING ONTO N; WE RECEIVED AN ADVISORY OF 'YOUR SEQUENCE IS ACR Y'. WE BOTH BELIEVED WE WERE FOLLOWING AN A320 WELL AHEAD ON N; AS THERE WAS NO OTHER ACFT IN SIGHT. APCHING #1 FOR TAKEOFF; WE RECEIVED 'TAXI INTO POSITION AND HOLD' (I BELIEVED RWY 12. THE DEP END OF BOTH RWYS SIT SIDE-BY-SIDE). THE CAPT WAS AT THIS TIME FINISHING UP THE TAKEOFF PA. AS WE CONTINUED TO ROLL FORWARD; SOMEONE ON THE FREQUENCY SAID 'THANKS ACR X YOU WERE SUPPOSED TO FOLLOW US.' IT WAS THEN THAT; I NOTICED THAT THE ACFT WE HAD BEEN FOLLOWING WAS ACFT Y (NOW BEGINNING THEIR TAKEOFF ROLL TO OUR R ON RWY 09L). MY ATTENTION WAS NOW DIRECTED TO CONSIDERATION OF THE PROCEDURAL REQUIREMENTS (TPS; VSPEEDS; RDO CHKLIST ITEMS; ETC). FOR THE CHANGE OF RWY; WHILE SIMULTANEOUSLY WONDERING HOW WE MAY HAVE FOULED UP OUR 'SEQUENCE TO FOLLOW.' TWR NOW ISSUED A TAKEOFF CLRNC FOR (I BELIEVE) RWY 12; WITH 'FLY HDG 120.' THE CAPT REJOINED THE FREQ AS I READBACK THE CLRNC AND HE CAUGHT THE FACT THAT WE HAD BEEN CLRED; THE HDG ASSIGNMENT AFTER TAKEOFF; BUT NOT THE RWY. HE ACKNOWLEDGED THE HEADING ASSIGNMENT TO ME; AND I BELIEVE THAT HE CAUGHT THE ENTIRE READBACK; SO I KEPT MY ATTENTION ON THE 'CHANGE-OF-RWY MATTERS. THE NEXT TIME I LOOKED UP; WAS WHEN THE CAPT SAID 'WHERE IS THIS GUY GOING.' (REFERRING TO AN ACFT ON APROX 3 MILE FINAL).I LOOKED UP; SAW WE WERE ACROSS THE HOLD LINE AND ASSESSED; 'LOOKS LIKE HE'S GOING TO RWY 12.' AS I RETURNED MY ATTENTION TO THE RWY CHANGE/TPS PREOCCUPATION; I HAD A SINKING FEELING. 'HOW CAN HE BE GOING TO RWY 12 WHEN THAT'S WHERE WERE SUPPOSED TO BE LINING UP RIGHT NOW.' THE CAPT BROUGHT THE TAXI TO A STOP JUST ACROSS THE ACTIVE SIDE OF THE HOLD LINE; AS WE BOTH SIMULTANEOUSLY REALIZED THAT THE LNDG ACFT WAS HEADING OUR WAY TO RWY 09L. THE TWR WAS ISSUING GAR INSTRUCTIONS TO THE LNDG ACFT BY THAT TIME. I QUERIED TWR TO CONFIRM WHETHER WE WERE CLEARED ONTO RWY 09L OR 12; AND HE CONFIRMED THAT IS WAS SUPPOSED TO BE RWY 12; BUT THAT WE WERE NOW 'CLRED FOR TAKEOFF ON RWY 09L; FLY HDG 120.' THE WHOLE INCIDENT TOOK ABOUT 40 SECS FROM THE TIME THE CAPT STARTED HIS PA TO THE TIME WE CROSSED THE HOLD LINE. I REALIZED THEN THAT I HAD ERRONEOUSLY BELIEVED THE CAPT WAS AWARE OF THE ENTIRE CLRNC; THAT I HAD NOT REPEATED THE CLRNC TO HIM UPON HIS RETURN TO THE FREQ; THAT I WAS HEADS-DOWN WITH OTHER CONCERNS WHILE I LEFT HIM TO TAXI THE ACFT ALONE; AND THAT I HAD BEEN CONSUMED WITH THE TECHNICAL REQUIREMENTS FOR THE CHANGE OF RWY; BUT NOT WITH MAKING SURE THE ACFT ACTUALLY GOT TO THE NEW RWY. I ALSO REALIZED HOW EASY IT WAS TO BECOME A PARTICIPANT IN AN UNINTENTIONAL RWY INCURSION. SUPPLEMENTAL INFO FROM ACN 541150: CLRED TO TAXI TO RWY 09L VIA TXWY N. APCHING RWY 09L I LEFT THE FREQ TO MAKE THE TAKEOFF PA. AFTER RETURNING TO TWR FREQ; I UNDERSTOOD CLRNC TO BE POSITION AND HOLD RWY 09L AND AFTER TAKEOFF FLY HDG 120 DEG AND I CONTINUED TAXIING TO RWY 09L. AT SAME TIME I SAW ACFT ON SHORT FINAL; BUT THAT ACFT APPEARED TO ME INITIALLY TO BE APCHING RWY 12; BUT WAS REALLY APCHING RWY 09L. I STOPPED MY ACFT AT THE EDGE OF RWY 09L AND THE OTHER ACFT WENT AROUND. TWR THEN CLRED US INTO POSITION AND HOLD ON RWY 09L AND PLAN HDG 120 DEG AFTER TAKEOFF. AT THIS POINT AND AFTER DISCUSSING THIS WITH THE FO; I STILL DO NOT RECALL RECEIVING A CLRNC TO RWY 12; AND I AM STILL NOT SURE WHERE THE MIS-COM OCCURRED.