Date: 201605
Local time of day: 1201-1800
Location: OAK.Airport, CA
Flight conditions: VMC
Weather elements / visibility: 10
Light: Daylight
Aircraft: Challenger 300
Operator: Air Taxi
Operating under: Part 135
Flight plan: IFR
Mission: Passenger
Flight phase: Initial Approach
Airspace: Class C OAK
ATC / advisory: TRACON NCT
Reporter organization: Air Taxi
Reporter function: Pilot Flying; Captain
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Confusion; Situational Awareness
Second reporter function: Pilot Not Flying; First Officer
Anomaly: Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance; Inflight Event / Encounter CFTT / CFIT
Detector: Automation Aircraft Terrain Warning; Person Air Traffic Control
When detected: In-flight
Result: Air Traffic Control Issued New Clearance; Flight Crew Became Reoriented
Contributing factors: Human Factors
Primary problem: Human Factors

Narrative: I am PF. Early accomplishment of APPROACH BRIEFING and FMS entries for Arrival for OAK OAKES2 with BANND transition fix and OAK ILS 28R as interim settings until further assignment. The above was completed (pre-empted) PRIOR to assignment of final transition and approach by NORCAL; therefore the VECTOR prompt was selected for the ILS with the expected resulting discontinuity between BANND and the ILS. I believe this to be normal practice. [In] other words; a discontinuity signifies a PENDING assignment. There was a discussion prompted by PNF as to why TOOOL fix was not posted yet with mutual conclusion that approach runway fix had not been entered yet (as expected). NORCAL issues 'OAKES2 arrival RWY 28 Transition' and to descend via the OAKES2. PNF updates the OAKES2 into the FMS but did not update the ILS 28R to include the transition fix resulting in arrival ending at BBUBB and the first fix in ILS starting at NIXDE. This update omission for the ILS is unnoticed by me; PF. Somewhere between fixes EVOLVE and BBUBB; we were cleared for the ILS 28R Approach. This clearance eliminates the possibility of a vectored and visual approach (nor did we specifically request such) and the mandatory nature of the transition fixes become heightened. Knowing our position relative to our clearance type; I call out to PNF to verify the correct legal transition because I did not want to go heads down (on charts at this altitude); than I added 'the last thing we want to hear from ATC is 'say position''. PNF asked me to check/verify NIXDE on FMS. I said OK believing it to be NAGVY. I fell into confirmation/expectation bias on similar name starting with N. From BBUBB inbound; indications that something was not correct was visual indication we were too close to terrain for a transition route followed by GPWS terrain alert; followed by ATC query regarding our position. NORCAL asked if we had OAK in sight and with affirm; cleared us for visual approach 28R.This a classic case of a few negative factors sneaking through our thoughtful diligent efforts. Self-analysis of positive factors are; this crew works well together; are having fun with our jobs; I felt alert and not fatigued. The CAUSE if this case is my failure to request/set aside an AMENDED BRIEFING event (and the corresponding FMS programming check) as soon as ATC assigned the runway transition.Contributing factors were:1. VMC weather creating expectation of visual approach.2. Programming and amending the FMS only when issued by ATC. This is correct but it does push programming time and attention to detail to a later time rather than earlier while in flight therefore compressing tasks depending on circumstance.3. [This aircraft] not having datalink to enable getting ATIS earlier and by text that can be read by both crew.4. Relatively new crew not having the general experience and the proficiency in particular FMS programming to appreciate the ramifications of nuanced errors; and ability to cope with correcting errors during time compressed event.5. Me; as copilot; OK'ed a flawed programming due to expectation/confirmation bias during a time compressed event. (A possible tweak for published charts is to avoid fixes with similar sounding names or starting with the same letter within the same transition/approach/proximity; similar contributing factor for [an air carrier flight] going into California with fix starting with 'R').The SOLUTION to this scenario is to increase diligence to AMENDED BRIEFING WITH CORRESPONDING FMS PROGRAMMING CHECK as soon as able when ATC amends the clearance. This will keep me out of time compression effects causing me to fall into expectation/confirmation bias events; and reminder to adjust more aggressively to cope with less experienced crew which is primary for an IOE/Standards captain; a position I enjoy and take seriously.


Second narrative: We were on the Oakland 2 arrival and upon reaching EVOLV we were cleared the ILS for 28R from the Oakland 2 arrival. The FMS had the ILS for 28R loaded in it already and per my Captain's request I sequenced the FMS. What I failed to realize is that it was loaded via vectors and not via the arrival. So we went to NIXDE instead of going to NAGVY. As we were getting close to NIXDE ATC gave us an altitude alert and informed us that we were below the MVA for that area. We informed him that we were VMC. He then told us that we were off course and asked us if we had the airport in sight. We told him we did and he then cleared us for the visual and handed us off to tower frequency. We flew the visual approach and landed without incident. Failure of knowing to reload the FMS with the arrival transition and failure of proper verification between crew members is what caused this situation. No matter what is going on we need to always take the time to verify clearances and both crew members need to verify that the FMS is loaded properly. My Captain had assumed that everything was loaded properly and when I failed to do it properly it cause this situation.


Synopsis: CL-300 flight crew on approach to OAK reported descending below the MVA and a GPWS terrain alert resulted related to an error in programming the FMS route.