COMMUTER SMT NON ADHERENCE TO ATC CLRNC UNAUTH RWY CROSSING DURING LNDG ROLL.

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AT APPROX 3 MI OUT ON FINAL FOR RWY 22L AT BOS WE WERE CLRED TO LAND. CLRNC WAS TO HOLD SHORT OF RWY 33L. I WAS PF AND COPLT WAS PNF. WE CROSSED RWY 33L AND TURNED OFF AT JULIET INTXN. THE LCL CTLR THEN STATED. 'YOU WERE TOLD TO HOLD SHORT OF RWY 33L BUT I DIDN'T NEED YOU TO ANYWAY; CONTACT GND 121.9.' I NEVER HEARD THE HOLD SHORT PART OF OUR CLRNC; ALTHOUGH THE COPLT SAID THAT HE DID. WHEN I ASKED WHY HE DIDN'T WARN ME HE SAID HE WAS UNFAMILIAR WITH BOS AND WAS MENTALLY THINKING OF RWY 27 TO HOLD SHORT OF. THIS MAKES SOME SENSE BECAUSE IT IS VERY COMMON TO GET A CLRNC TO HOLD SHORT OF RWY 27 WHEN LNDG ON RWY 22L; BUT VERY UNUSUAL TO RECEIVE A CLRNC TO HOLD SHORT OF RWY 33L. I BELIEVE THIS WAS CAUSED BY POOR CREW COORD AND WE WERE VERY LUCKY NOT TO HAVE HAD AN INCIDENT OR WORSE. CAPT (ME) SHOULD REMEMBER TO STAY EXTREMELY ALERT DURING APCH AND LNDG PHASE OF FLT. COPLT ON TEMPORARY DUTY FROM FL AND UNFAMILIAR WITH AREA. COMPLEX ARPT LAYOUT. CAPT NEW IN ACFT. DREW HAVING A SOMEWHAT ADVERSARY RELATIONSHIP DUE TO RECENT ONGOING MERGER BTWN ACR X AND ACR Y AIRLINES. HIGH NOISE LEVEL IN ACFT. VERY POOR CREW COORD TRNING AT ACR X AIRLINES AND CRM TRNING NONEXISTENT.