MSN ACR DEP ISSUED CLRNC TO TAXI TO RWY 21 WAS QUESTIONED BY ATC CROSSING RWY 18; TAPE REVIEW CONFIRMED CLRNC WAS TO RWY 21.

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AFTER PUSHBACK IN MSN; CONTACTED GND FOR TAXI. WAS INSTRUCTED BY GND 'ACFT X TAXI RWY 21.' I (THE FO) READ BACK THAT INSTRUCTION. AFTER LOOKING AT THE ARPT DIAGRAM; CAPT EXPLAINED TO ME THE RTE HE PLANNED TO TAKE TO RWY 21 AND I AGREED. XING RWY 18 ON THE WAY TO RWY 21; ATC QUERIED US ASKING 'ACFT X; DO YOU KNOW YOU JUST CROSSED RWY 18?' IMMEDIATELY; I REPLIED AFFIRMATIVE; THAT WE HAD TO CROSS RWY 18 IN ORDER TO ARRIVE AT RWY 21. GND CTL THEN SAID THAT WE WERE INSTRUCTED TO TAXI TO RWY 18. AT THIS POINT; THE CAPT INFORMED ATC THAT WE WERE IN FACT TOLD TO TAXI TO RWY 21. BOTH RWYS WERE ACTIVE. THE MOST RECENT ATIS DID SAY THAT BOTH RWY 21 AND RWY 18 WERE BEING USED. AT THAT TIME; CAPT ASKED FOR A NUMBER FOR THE TWR FACILITY TO FIGURE OUT THE CLRNC WHEN WE ARRIVED BACK IN ZZZ. NO FURTHER EVENT OCCURRED. ONCE AT THE GATE IN ZZZ; CAPT CALLED THE ATC FACILITY. AT THAT TIME THEY INFORMED US THAT THEY HAD CHKED THE TAPES AND THAT WE WERE IN FACT TOLD TO TAXI TO RWY 21. THEY ALSO SAID THAT NO AIRPLANE WAS ON FINAL APCH OR DEPARTING SO IT WAS ONLY A MINOR INCIDENT. GND CTL INFORMED US TO TAXI RWY 21; WHICH WE READ BACK. HOWEVER; THEY MUST HAVE MEANT TO SAY RWY 18; AS THEY QUESTIONED WHEN WE CROSSED RWY 18 ON THE WAY TO RWY 21. IN MY OPINION; THIS EVENT COULD HAVE HAPPENED BECAUSE THE 2 PREVIOUS ACFT TO CONTACT GND CTL WERE SMALL GA ACFT; WHO WERE BOTH INSTRUCTED TO TAXI TO RWY 21. THEN WE CALLED IMMEDIATELY FOLLOWING THOSE ACFT. ALTHOUGH GND CTL MADE A MISTAKE; I FEEL AS THOUGH I COULD HAVE TAKEN ANOTHER STEP AND QUESTIONED ATC. I HAD NEVER BEEN ISSUED A DEP OUT OF MSN FROM THE SMALLER RWY 21. IT CONFUSED ME A LITTLE AND I SHOULD HAVE ABSOLUTELY CONFIRMED THAT ATC IN FACT WANTED US TO TAXI TO RWY 21. IF I WOULD HAVE SIMPLY ASKED; ATC WOULD HAVE TOLD US TO TAXI TO RWY 18. I LEARNED THAT IF I EVER AM CONFUSED BY AN OUT-OF-THE-ORDINARY INSTRUCTION; I SHOULD SIMPLY ASK ATC TO MAKE SURE IT IS; IN FACT; WHAT THEY WANT US TO DO.