Date: 201810
Local time of day: 1801-2400
Location: SAN.Tower, CA
Aircraft: Light Transport; Low Wing; 2 Turbojet Eng
Flight plan: IFR
Flight phase: Initial Climb
Airspace: Class B SAN
ATC / advisory: Tower SAN
Second aircraft: B737 Undifferentiated or Other Model
Reporter organization: Government
Reporter function: Supervisor / CIC
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Communication Breakdown; Confusion; Situational Awareness; Human-Machine Interface
Anomaly: ATC Issue All Types; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Person Air Traffic Control
When detected: In-flight
Contributing factors: Equipment / Tooling; Human Factors; Procedure
Primary problem: Procedure

Narrative: I was CIC (Controller In Charge) and monitoring operations; specifically Local control. LC (supervisor working LC) stated that his upwind guy (Aircraft X) wasn't doing what he should and was supposed to be a PADRZ departure (which is to the northwest). I looked at the radar nearest which is at LC position. There is no radar at the supervisor desk as our tower is under construction. The guy was untagged and turning southwest bound toward an already departing Aircraft Y. Everyone in the cab; GC (Ground Control) CD (Clearance Delivery) LC immediately tried to investigate what happened. LC stated that he notified SoCal W sector that the guy did not tag up on his correct code and should be a PADRZ departure. Ground then brought over a second strip on Aircraft X that had a different destination and was a ZZOOO departure which goes straight out and then south to east. CD stated that they read a clearance [for a] PADRZ departure. CD did not read the other clearance [of] ZZOOO but a previous controller had read it based on strip marking. What appeared to happen then was that two clearances were read at different times to Aircraft X by different controllers and the pilot never said that he had a previously filed clearance read to him to a separate destination. Ground had both strips at one time and due to the workload and many GA strips; may not have noticed both strips. Local ran down the PADRZ departure strip and notified SoCal as soon as the plane didn't tag up and appeared off course. Also; GA targets commonly do not tag up on our ASDE-X until airborne.This seemed to be a perfect storm of events. Two different controllers read clearances to the pilot at different times. The FDIO [Flight Data Input Output] software apparently does not pop a DUP [Duplicate] or MUL [Multiple] warning for clearances that are read; only if they are PDC or CPDL capable. Then ground was busy and had both strips at some point but no warning from pilot about two destinations filed. The ASDE never tagged up the planes beacon but it's become common at SAN to expect the tag up on the upwind and never on ground with GA on the north side of the airport.While it's easy to say that CD or GC should catch the double strip; it can very easily slip through as what just happened; whether due to workload or controller change. I think the FDIO system should have some function to always warn of an aircraft callsign being issued on more than one flight plan. That would help us the most. The pilot not saying he filed two destinations did not help either.




Synopsis: SAN Tower Controller reported confusion handling an aircraft that had filed multiple flight plans.