Southwest Airlines canceled several hundred flights Monday as it worked to resolve the problems that led it to strike more than a quarter of its scheduled flights over the weekend.

The cancellations wreaked havoc on travel plans for thousands of passengers. At least some were trying to make it to the Boston Marathon.

Southwest blamed the cancellations on several causes, including problems with the weather and air traffic control Friday and an inability to get flight crews and planes to where they were needed.

Cancellations Friday, primarily caused by severe weather, prevented planes and crews from being where they needed to be on Saturday, a cascading problem that led to cancellations and delays throughout the weekend and into Monday, the airline said.

The airline’s share price fell more than 4% Monday.

Disruptions were minimal at Seattle-Tacoma International Airport, spokesman Perry Cooper said. The cancellations affected seven or eight Seattle flights each day over the weekend, a tiny percentage of the airport’s more than 1,100 flights per day.

The airline and the union that represents its pilots took pains throughout the weekend and Monday to say that the disruption was not caused by protests over the airline’s recently announced vaccination mandate, denying an idea, fueled by some early news reports, that had gained traction online among conservatives and anti-vaccination activists.

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The Federal Aviation Administration acknowledged that flights were delayed or canceled Friday because of severe weather, military training exercises and a brief staffing shortage at one air traffic control center but said that the disruption lasted only a few hours.

Casey Murray, president of the Southwest Airlines Pilots Association, dismissed the idea that pilots had called in sick to protest the company’s vaccine mandate, though the union has asked a court to prevent Southwest from enforcing that requirement. Pilots called in sick at a normal rate this weekend, he said.

Instead, Murray said, the widespread cancellations were caused by technological issues and problems with how pilots are reassigned and rerouted during disruptions, a process complicated by Southwest’s uniquely large, point-to-point network. In a typical day, about 10% of pilots are reassigned from the flights they were scheduled to operate. That figure was 71% on Saturday and 85% on Sunday, according to Murray.

Seattle Times staff contributed to this report.