Citation Excel (C560XL)
Flight Crew Multiengine; Flight Crew Air Transport Pilot (ATP); Flight Crew Instrument
Flight Crew Last 90 Days 70; Flight Crew Total 14369; Flight Crew Type 1864
Workload; Time Pressure; Communication Breakdown; Confusion; Distraction
ATC Issue All Types; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Flight Crew Returned To Clearance; Flight Crew Became Reoriented
Procedure; Human Factors
We were flying into SFO on the BDEGA1 RNAV arrival. We were proceeding direct to LOZIT intersection descending to 15;000 ft. ATC was Oakland Center. We were then directed to 'Descend Via the BDEGA1 RNAV arrival.' Prior to BDEGA we were handed off to NorCal approach. On initial contact the controller said; 'Landing 28L; expect visual 28L'; we responded with; 'Roger; 28L'. We crossed CORKK at 11;000 ft and were directed to slow to 210kts at that point. After CORKK we incorrectly flew the 28R transition that was preprogrammed into the FMS instead of the 28L transition which would have continued on the same heading; we made a slight left turn at CORKK. The controller advised us shortly after passing CORKK that we were flying the 28R transition and to turn right direct to SFO and expect vectors for the visual approach for 28L. The controller then said we had an aircraft deviation and needed to contact them at XXX-XXX-XXXX once on the ground. We had preloaded runway 28R into the FMS to load the arrival since we were approaching from the North. You cannot put the arrival in the FMS without selecting a runway transition. We did not catch the transition change when we checked into NorCal approach approximately 3 minutes before reaching CORKK.  If the controller would have said; 'Fly the 28L transition;' this would have been a trigger to check the FMS. No expected runway was given until very close to CORKK. Upon contacting NorCal approach on the ground the supervisor on the phone took my name; address and ATP certificate number. He said initially they cannot really discuss the event; just take the information. After he received the information he was a little more open to talk about the event.  He said this has been a very common problem and has happened a lot since this arrival was created. He also checked the tapes quickly to verify the controller and pilot dialogue. He also told me to contact the Quality Control supervisor to get more information. I contacted the Quality Control supervisor about the event. [Supervisor] also expressed how often this has been happening with this new arrival and how it could be confusing to change transitions at the last minute. [Supervisor] agreed that not using the term '28L Transition' could be confusing since this is one of the common ways to issue this clearance. [Supervisor] also said the BDEGA1 RNAV arrival is being updated because of this issue; and soon they are eliminating the specific runway transitions with this change. [Supervisor] also verified the recorded dialogue and distance from CORKK when we received the specific runway assignment. In hindsight we should have anticipated the possibility of a runway change and confirmed the transition to be flown in the FMS well before getting to CORKK. Upon hearing runway 28L from the controller we looked up the new localizer frequency; but we did not follow up and look at the STAR to see if there were changes based on 28L that needed to be entered into the FMS.
A CE-560XL flight crew flying the BDEGA1 STAR into SFO were given a late runway change and neglected to insert the new transition into the FMS.  ATC notified them that they had gone off course.