RWY INCURSION; ACR X HAD LTSS FROM CPR Y AND SMA Z. SYS ERROR.

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WHEN I ASSUMED THE GND CTL POS; ACR X WAS HOLDING SHORT OF RWY 15 ON GND FREQ. THE LCL CTLR ADVISED ME 'CROSS RWY 15; TWICE.' I INSTRUCTED ACR X TO CROSS RWY 15; AND THEN INSTRUCTED AN SMA Z TO FOLLOW. AFTER A FEW XMISSIONS TO OTHER ACFT; ACR X ADVISED ME 'WE'RE HOLDING SHORT; YOU CLRED US TO CROSS. THAT WOULDN'T HAVE BEEN A GOOD IDEA.' I THEN OBSERVED CPR Y MIDFIELD. IT HAD DEPARTED RWY 15. I ADVISED ACR X TO 'HOLD HIS POS.' AFTER A FEW XMISSIONS TO OTHER ACFT; ACR X ADVISED ME HE WAS OVER THE HOLD SHORT LINES FOR RWY 15. I IMMEDIATELY ADVISED THE LCL CTLR 'I'M HOLDING THE 2; BUT ACR IS OVER THE HOLD SHORT LINES.' LCL NODDED IN THE AFFIRMATIVE AND SAID; 'I KNOW; I KNOW.' BY THIS TIME; TFC WAS BUILDING (DEPS) AND APCH CTL HAD PUT A STOP ON W DEPS. ACR X WAS A W DEP. A FEW MINS LATER; ACR X ADVISED 'GND; I TOLD YOU WE ARE OVER THE HOLD LINES. IF YOU ARE GOING TO KEEP USING THIS RWY; WE NEED TO BE MOVED.' I THEN OBSERVED AN SMA Z ROTATING ON RWY 15. I AGAIN; ADVISED LCL OF ACR X POS AND LCL TOLD ME TO 'CROSS RWY 15.' AT NO TIME BTWN THE FIRST AND SECOND XING THAT LCL GAVE ME; DID I RPT CLR OF RWY 15; AND DURING THAT TIME; 2 TKOF CLRNCS WERE ISSUED FOR THAT RWY. I DON'T KNOW IF THIS COULD HAVE BEEN PREVENTED. THIS WAS HUMAN ERROR. HOWEVER; THERE IS QUESTION AS TO WHO SAID WHAT BTWN THE GND AND LCL CTLRS. IF THIS TYPE OF COORD WAS REQUIRED TO BE DONE ON THE OVERRIDE LINES (RECORDED); THERE WOULD BE NO QUESTION. SUPPLEMENTAL INFO FROM ACN 259095: AFTER HOLDING SHORT OF RWY 15 ENRTE TO RWY 18; WE AND ANOTHER ACFT BEHIND US WERE GIVEN CLRNC TO CROSS RWY 15. AS WE APCHED THE RWY; A SMALL JET IN POS ON RWY 15 STARTED ITS TKOF ROLL. WE STOPPED SHORT OF THE RWY EDGE LINE. BUT WELL OVER THE HOLD LINE. AFTER ADVISING GND CTL OF THE TKOF; WE THEN ADVISED GND CTL THAT WE WERE OVER THE HOLD LINE. TWR THEN DEPARTED ANOTHER SMA Z ON RWY 15. WE AGAIN ADVISED GND CTL THAT WE WERE OVER THE HOLD LINE AND REQUESTED TO TAXI CLR OF THE RWY. WE WERE THEN CLRED TO CROSS RWY 15. OBVIOUSLY; THE NEAR MISS WITH THE DEP JET WAS A MISCOM WITH GND CTL AND TWR. HOWEVER; EITHER PROC NEEDS TO BE CHANGED OR THEY WERE NOT FOLLOWED WHEN THE TWR DEPARTED ANOTHER ACFT AFTER WE RPTED THAT WE WERE OVER THE HOLD LINE. ALL OPS SHOULD BE STOPPED IMMEDIATELY WHEN ANY RWY INCURSION TAKES PLACE; AND RESUMED ONLY AFTER A SUPVR ASCERTAINS THROUGH DIRECT RADIO CONTACT THAT ALL ACFT INVOLVED ARE IN SAFE POS CLR OF THE RWY.