Date: 202104
Local time of day: 0601-1200
Location: FAI.Airport, AK
Aircraft: Commercial Fixed Wing
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Initial Approach
Airspace: Class D FAI
ATC / advisory: TRACON FAI
Reporter organization: Air Carrier
Reporter function: First Officer; Pilot Not Flying
Human factors: Workload; Situational Awareness; Human-Machine Interface; Confusion; Troubleshooting
Second reporter function: Captain; Pilot Flying
Anomaly: Deviation / Discrepancy - Procedural Published Material / Policy; Inflight Event / Encounter CFTT / CFIT
Detector: Automation Aircraft Terrain Warning
When detected: In-flight
Result: Air Traffic Control Provided Assistance; Flight Crew FLC complied w / Automation / Advisory; Flight Crew Became Reoriented; Flight Crew Returned To Clearance
Contributing factors: Human Factors; Procedure; Software and Automation
Primary problem: Software and Automation

Narrative: On the LIBER 3 arrival; ATC instructed 'after GLOWS fly heading 020 descend 4200 ft. for traffic; vectors for the approach.' Approximately 15 miles from the runway; ATC instructed '5 miles from CIGNI left turn to intercept the inbound course; maintain 4200 until established; cleared approach.' PF (Pilot Flying) tuned heading; drew a line out from WUNDU; set 1700 in the altitude alert and armed the approach.As course came alive and captured we noticed path continuing to drop below us on the vertical guide. As course came alive; PF pushed VS then VNAV. ALT turned to FLCH and the aircraft began to descend. Rather than capture; it descended through the path. PF pushed VS in attempt to regain the path. We heard 'Terrain warning.' PF turned off AP; began a climb and asked PM (Pilot Monitoring) to rest 4;200. ATC questioned the low altitude alert and asked us to confirm we were established on the approach due to the MSA of 4;200. We confirmed due to laterally established and visual contact with terrain. PF leveled at 4;200; engaged AP and we worked to re-engage the APP while continuing; landed and debriefed.After being vectored off the arrival; it may have been a better course of action to load the RNAV Y for 20R due to better altitude protections. Also need to wait for LNAV to be in magenta.


Second narrative: Due to traffic we were on a heading and descended to 4;200. 5 miles from CIGNI turn left maintain 4;200 until established; cleared approach. I turned to the heading; pressed approach and spun the AA down to 1;700 and lined out from WUNDU; entered in the inbound course and activated.Waiting to intercept I noticed VNAV path was dropping below us. I as saw the course come alive I pressed VS and VNAV; ALT turned to FLCH. Aircraft began a descent to capture PATH but we went through it. My first reaction was to press VS and climb back to path. We heard a terrain warning; I clicked AP off and began a climb asked PM (Pilot Monitoring) to spin AA to 4;200. ATC notified us of a Low Altitude alert; he said if we were established we were okay; We were laterally established and had visual contact with all terrain. I leveled at 4;200 and engaged autopilot. We worked to re-engage APP and continued.We landed and debriefed. Mistake was lowering AA to 1;700 until fully magenta.


Synopsis: Air carrier flight crew reported the auto pilot was not programmed correctly for the approach and the aircraft descended below the Minimum Safe Altitude.