Southwest's weekend meltdown wasn't due to a vaccine protest, its pilots union says

• Southwest Airlines canceled nearly 2,000 flights over the weekend due to staffing shortages.
• High-profile public figures incorrectly suggested the shortages were due to an anti-vax walkout.

Southwest Airlines canceled nearly 2,000 flights over the weekend due to a confluence of severe weather and air traffic control issues, leaving thousands of travelers stranded.

The company's pilots union said the issues were not due to a pilot protest, dispelling misleading tweets from high-profile public figures, including Republican lawmakers.

The Federal Aviation Administration added that a military training exercise and limited staffing at one control tower exacerbated the issue for a few hours on Friday, but that the problems did not cause the ripple effect into the weekend.

"Some airlines continue to experience scheduling challenges due to aircraft and crews being out of place," the agency said Sunday.

The weekend meltdown came just a day after the airline's pilot union asked a court to block the company from carrying out President Joe Biden's vaccine mandate while a lawsuit over an alleged labor laws violation is disputed. The union argued the federal order violates the Railway Labor Act, which controls airline-union relations.

The previous week, Southwest had announced all employees must be vaccinated by November 24.

Headlines about the new rules and friction with its union prompted a handful of public figures to incorrectly suggest flight crews were calling out of work in an anti-vax protest.

"Joe Biden's illegal vaccine mandate at work! Suddenly, we're short on pilots & air traffic controllers," Texas Sen. Ted Cruz, a Republican, tweeted Sunday.

Meanwhile, former Fox News producer Jillian Anderson, conservative author Brigitte Gabriel, and podcast host Jesse Kelly also pushed the narrative, with Kelly saying "cancel my flights -- continue the fight."

The union rebutted the swirling false information, saying Saturday its pilots were not participating in any "official or unofficial job actions," which could refer to a strike, sickout, or walkout.

"SWAPA is aware of operational difficulties affecting Southwest Airlines today due to a number of issues, but we can say with confidence that our Pilots are not participating in any official or unofficial job actions," it said. "Our Pilots will continue to overcome SWA management's poor planning, as well as any external operational challenges, and remain the most productive Pilots in the world."

Southwest echoed SWAPA and emphasized that the flight disruptions were due to bad weather and ATC issues in Florida.

"The weekend challenges were not a result of Employee demonstrations, as some have reported," Southwest told Insider.

Flight disruptions due to staffing shortages and weather are nothing new in the airline industry, where small blips in highly coordinated schedules can cause cascading delays.

In a note to staff seen by CNBC, Southwest executive vice president of daily flight operations Alan Kasher said displaced pilots, coupled with federal and contractual working limits, can cause a quick snowball effect.