ACR DEP FROM MWA WAS CLRED FOR TKOF; CROSSED HOLD LINE; ONLY TO SEE ACFT ON FINAL EXECUTING GAR; TWR ADMITTED ERROR; NO OPERROR RECORDED.

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OPERATING AS A CREW OF 2 AS A SCHEDULED PART 121 FLT FROM MWA-ZZZ. UPON CALLING FOR TAXI AND REQUESTING CLRNC; MWA GND CTL ADVISED US TO TAXI TO RWY 2 VIA THE APPROPRIATE TXWYS AND CLRNC WAS ON REQUEST. WE REMAINED ON THE GND FREQ AWAITING THE IFR CLRNC. AFTER AN UNEVENTFUL TAXI TO RWY 2 WE WERE HOLDING SHORT OF THE RWY AT THE DEP END WHEN THE CLRNC BECAME AVAILABLE. ATC READ US THE CLRNC WHICH WAS AS FILED AND IT WAS READ BACK. AFTER A REVIEW OF THE CLRNC; THE BEFORE TKOF CHKLIST WAS COMPLETED AND WE SWITCHED FREQS TO THE TWR AND ADVISED READY FOR TKOF. PRIOR TO THIS POINT; WE WERE ONLY MONITORING THE GND FREQ AND DID NOT HEAR ANY TWR XMISSIONS. THE TWR CLRED US FOR TKOF AND 'CLRED ON COURSE.' AS IS CONSISTENT WITH COMPANY PROCS; THE FO VISUALLY CLRED THE R SIDE OF THE ACFT AND I VISUALLY CLRED THE L AND THIS WAS ACKNOWLEDGED VERBALLY. AT THIS TIME (ABOUT 3-5 FT ACROSS THE HOLD SHORT LINE AND PRIOR TO ENTERING THE RWY ITSELF) I DENOTED TFC ON THE TCAS DISPLAY +400 FT ON FINAL FOR OUR RWY. I IMMEDIATELY STOPPED THE ACFT AND SIMULTANEOUSLY INQUIRED WITH THE TWR AS WELL AS VISUALLY BEGAN SCANNING THE FINAL APCH PATH AGAIN. I THEN SAW A SMALL SINGLE ENG GA ACFT ON FINAL (LATER SEEN TO BE A BONANZA) WITHOUT A LNDG LIGHT MAKING HIM A 'SPEC' WHEN LOOKING HARD. THE TWR ADVISED US TO HOLD SHORT OF THE RWY AND I REPLIED THAT WE WERE ALREADY ACROSS THE HOLD SHORT LINE. THE BONANZA WAS THEN HEARD ON THE TWR ADVISING HE WAS INITIATING A GAR. THE TWR NEVER GAVE HIM A GAR INSTRUCTION. WE WERE SUBSEQUENTLY CLRED FOR TKOF AGAIN AND THE TWR STATED 'SORRY ABOUT THAT.' THERE WAS NO FURTHER INCIDENT. IN THIS OCCURRENCE THE COMPANY PROCS FOR MAINTAINING VIGILANCE ENTERING A RWY WERE EFFECTIVE IN PREVENTING MORE OF A CONFLICT THAN THAT WHICH OCCURRED. THE BONANZA PLT'S SELF INITIATION OF A GAR WAS THE RIGHT MOVE; HOWEVER; IT WOULD HAVE BEEN BETTER HAD THE OTHER PLT BEEN PROACTIVE IN AN INQUIRY OF THE TWR AFTER HEARING US CLRED FOR TKOF ON HIS LNDG RWY. THE TWR WAS IN ERROR BY CLRING US FOR TKOF.