Date: 201403
Local time of day: 1801-2400
Location: SAN.Airport, CA
Aircraft: A319
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Flight phase: Descent
Airspace: Class B SAN
Aircraft component: Autoflight System
Component problem: Design
Reporter organization: Air Carrier
Reporter function: Pilot Flying; Captain
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Distraction; Confusion; Communication Breakdown; Training / Qualification; Workload
Second reporter function: First Officer; Pilot Not Flying
Anomaly: Aircraft Equipment Problem Critical; Deviation - Altitude Crossing Restriction Not Met; Deviation - Altitude Overshoot; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance
Detector: Person Air Traffic Control
When detected: In-flight
Result: Air Traffic Control Issued Advisory / Alert
Contributing factors: Aircraft; Chart Or Publication; Human Factors; Procedure
Primary problem: Aircraft

Narrative: In anticipation of Runway 27 arrival; the RNAV 27; LYNDI THREE arrival; with TNP transition was entered into the MCDU prior to top of descent and briefed. What occurred on the arrival profile and not discovered was waypoint LUCKI with crossing constraint at or above 6100' was dropped out and replaced with ZUSUB with crossing constraint at or above 5300'. All other waypoints and constraints on the LYNDI THREE arrival remained as published. SOCAL Approach cleared us to fly the RNAV 27 approach after LYNDI. Descent was performed in managed descent mode and we crossed ZUSUB at 5300' and LYNDI at 5000' before selecting APPROACH mode. ATC informed us at this point that we had missed the LUCKI crossing constraint of 6100' but this happens quiet often and was not a problem. After landing we re-entered the arrival and discovered LUCKI intersection had been replaced with ZUSUB intersection with a lower altitude crossing restriction. Why was this approach constructed this way? It is a built in trap.Do not fly the RNAV 27 approach! In order to comply with the LYNDI THREE arrival you have to manually delete ZUSUB intersection and manually insert LUCKI intersection with it's 6100' crossing restriction. This is contrary to how we normally load the MCDU and brief prior to top of descent in that it requires manual re-insertion of one published crossing restriction out of several on a busy arrival procedure. The San Diego company page/chart should have a note of caution regarding this situation.


Second narrative: Before descent descending into SAN via the LYNDI THREE ARIVAL we requested and got approved for the RNAV 27 instead of the LOC 27. The RNAV 27 (without any via's [transitions]) was then inserted into the MCDU; briefed; and all fixes on the approach were verified. At this point the LYNDI THREE ARRIVAL had already been briefed and all fixes and crossing restrictions verified at least twice. It was my assumption that inserting a new approach (without a via) into the MCDU would not affect the arrival. I was wrong. The 8;000 FT crossing restriction at BARET and the fix LUCKI were removed from the arrival and led to an altitude deviation as the aircraft descended to the MEA of 5;300 FT as depicted on the RNAV 27 approach plate between BARET and ZUSUB. We were instructed by ATC that we were cleared for the RNAV 27 [only] after descending via the LYNDI THREE and crossing BARET. We briefed and did not select the APPR push button until we had crossed BARET. The entire descent was flown in managed mode. Before being switched to Lindbergh Tower; SOCAL Approach advised us that he believed we started the approach before BARET which resulted in an altitude deviation. He also commented this was a common error they have been seeing. Pilots must pay special attention that LUCKI (and its crossing restriction) and the crossing restriction at BARET are present as they seem to be getting dropped out of the arrival when inserting the RNAV 27 (without a via). It would make sense to me that LUCKI would be dropped if BARET was entered as an approach via as LUCKI is not part of the RNAV 27 as depicted on its approach plate. However; in our case; LUCKI was deleted even without selecting BARET as a via. Once we arrived at the gate in SAN; we rebuilt the LYNDI THREE and RNAV 27 in the MCDU [again] 'without a via' and LUCKI was again dropped.


Synopsis: An A319 flight crew who had programmed the LYNDI RNAV STAR and the RNAV (GPS) Runway 27 approach to SAN were surprised when Approach Control advised they had failed to comply with STAR altitude restrictions at BARET and LUCKI waypoints and that LUCKI had; in fact; turned itself into the nearly co-located ZUSUB; a fix on the RNAV (GPS) approach. Review after landing determined that the waypoints and their restrictions on the STAR had autosequenced to 'similar' ones on the IAP but which included crossing altitudes of as much as 2;700 FT lower than their equivalent STAR crossings. Although they had not selected a 'VIA' mode; the changes were unilaterally (and repeatedly) altered by the FMGC.