Date: 201909
Local time of day: 0601-1200
Location: MYF.Airport, CA
Flight conditions: VMC
Light: Daylight
Aircraft: Small Aircraft
Operator: Personal
Operating under: Part 91
Flight plan: VFR
Mission: Personal
Flight phase: Landing
Airspace: Class D MYF
ATC / advisory: Tower MYF
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Situational Awareness
Second reporter function: Local
Anomaly: ATC Issue All Types; Aircraft Equipment Problem Less Severe; Deviation / Discrepancy - Procedural Published Material / Policy; Ground Excursion Runway; Ground Incursion Runway
Detector: Person Air Traffic Control
When detected: Taxi
Contributing factors: Aircraft; Company Policy; Procedure; Human Factors
Primary problem: Company Policy

Narrative: I came to the tower cab from my break as the event was starting. Aircraft X was on landing rollout for Runway 28R and turning right onto Runway 23; which I immediately recognized as abnormal because all parking is to the left. I grabbed the binoculars and saw Aircraft X's right main tire was flat; which is why the aircraft was turning right; the only way the pilot could turn. The aircraft came to a stop on the shoulder of Runway 23; fairly close to the runway edge of Runway 28R at an unknown distance. I noticed the CIC (Controller in Charge) was combined with Ground Control and busy so I grabbed my headset and called Airport Operations to notify them of the disabled aircraft. No one in the tower at the time of the event saw a need to stop using Runway 28R as we have vehicles occasionally operating up the edge and it hasn't been an issue. We simply provide an advisory to the landing and departing aircraft. We also had a helicopter operating on the numbers of Runway 23 that nobody considered an issue; as the helicopter can easily remain at least 200 feet away from the disabled aircraft and the normal pattern already keeps them at least 200 feet away anyway.I took the CIC/Ground position about 5 minutes after the event. I asked the Airport Operations personnel that were on site to estimate how far off of the runway the disabled aircraft was and they told me about 30 feet. The disabled aircraft sat in that location for about 45 minutes before a tow vehicle could move it. About 20 minutes after the event started; one of our Supervisors and the Air Traffic Manager (ATM) came to the tower. Neither of them said anything about not using Runway 28R; nor did the Airport Operations personnel on site. Several days later I get a call from our ATM that Quality Assurance from the Western Service Area had a big problem with the way the event was handled; and that every single aircraft that landed or departed on Runway 28R during the time the disabled aircraft was in the runway safety area is considered a runway incursion. Also; every time the helicopter operated on the numbers of Runway 23 was also a runway incursion. This is news to me as I suspect its news to everyone else here including management. We obviously need facility wide training on this sort of contingency. I'm also wondering what is Airport Operation's responsibility in this sort of scenario? Aren't they supposed to tell us a runway is closed or open?


Second narrative: [Report narrative contains no additional information.]


Synopsis: Tower Controllers reported they continued to use a runway after a landing aircraft had become disabled and left the runway. They were informed later that continued operation constituted runway incursion violations.