MD90 ACFT ON STAR. APCH CTLR GAVE A DIRECT CLRNC; BUT FLC DIDN'T HEAR IT AND ASKED TO REPEAT. APPARENTLY IN THE REPEAT CLRNC THE CTLR FORGOT TO INCLUDE THE DIRECT CLRNC. FLC RECEIVED TCASII RA REQUIRING DSCNT AND CTLR INTERVENED QUESTIONING THEIR HEADING AT WHICH TIME THE CTLR CLARIFIED THE DIRECT CLRNC.

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INBOUND TO SNA FROM PSP VIA THE KAYOH 3 STAR. AFTER XING 'BANDS' INTXN AT 14000 FT MSL WE WERE GIVEN A FREQ CHANGE TO SOCAL APCH. THE CTLR GAVE US SOME INSTRUCTIONS AND THE LCL ALT SETTING. NEITHER OF US COULD MAKE OUT ANYTHING BUT THE ALT SETTING; SO I ASKED THE COPLT TO REQUEST FROM THE CTLR A REPEAT OF HIS INSTRUCTIONS. HE REPLIED THAT AFTER KAYOH INTXN WE WERE CLRED TO RESUME THE KAYOH ARR. THAT WAS PROBABLY MY FIRST 'FLAG.' WHILE IT SEEMED THAT SOMETIMES ON THIS PARTICULAR ARR WE WERE CLRED DIRECT TO KAYOH (BYPASSING HOMELAND-HDF) I HAD ASKED FOR AND HAD GOTTEN A REPEAT OF THE CTLR'S INSTRUCTIONS SO I CONVINCED MYSELF THAT WE WERE DOING WHAT WE WERE INSTRUCTED TO DO. SUBSEQUENTLY WE WERE CLRED TO 8000 FT. WHILE IN A DSCNT THROUGH 10500 FT WE FIRST GOT A TA AND LATER AN RA. I INCREASED THE DSCNT RATE AND HAD VISUAL CONTACT WITH THE CLBING TWIN OTTER. THE CTLR GAVE US AN IMMEDIATE R TURN AND THEN ASKED IF WE WERE GOING DIRECT TO KAYOH. REALIZING WHAT HAD HAPPENED BACK WITH THE REPEATED RADIO CALL; I TOLD THE CTLR WHAT WE HAD HEARD ON THE SECOND XMISSION (HE APPARENTLY FAILED TO REPEAT THE CLRNC DIRECT TO KAYOH THIS SECOND TIME). PERSONALLY I SHOULD HAVE QUESTIONED THE CTLR FURTHER AFTER THE INITIAL CONFUSION AND THE 'RESUME THE KAYOH ARR' SHOULD HAVE GIVEN ME ANOTHER HINT.