Southwest cancelled more than 360 flights on Monday — 10% of the day’s schedule — and over 800 were delayed, according the FlightAware tracking system.

Southwest Airlines Co. shares briefly plunged more than 4%, but they recovered somewhat by the afternoon. They were down 3% by the afternoon.

Shortly after the airline ordered that all employees be vaccinated against COVID-19, widespread disruptions started. Although the union stated that it does not oppose vaccination, it claimed in its filing that Southwest must negotiate before it takes such a step.

Reports that pilots were protesting the vaccine mandate caused by a sickout or slowdown by the union were denied. The union stated that it “hasn’t authorized and will not condone any job action.”

Another explanation was offered by the pilots association: Southwest’s operation had “become brittle and subjected to massive failures under slightest pressure” due to a lack support from the company. The union lamented the “already strained” relationship between the company and it.

During the pandemic, thousands of workers were persuaded by airlines to take leave of absence. American and Southwest Unions argued that management was too slow in bringing back pilots, leaving them short-handed.

Southwest’s executive vice-president of daily operations Alan Kasher said that the airline had been staffed for the weekend, but was caught up in air-traffic control problems and bad weather in Florida, and couldn’t recover fast. He noted that the airline had fewer flights available to accommodate passengers who were stranded because of the cutbacks made during the pandemic.

Chris Mainz, spokesperson for Southwest, stated that “the weekend challenges were not the result of Southwest employee demonstrations.”

Because they are federal contractors, the White House pushes airlines to comply with vaccine mandates. They get paid by the Defense Department for operating flights that have carried Afghan refugees to the U.S. in this summer’s summer.

United Airlines was the first major U.S. airline to announce a vaccination requirement. Even after President Joe Biden’s order to federal contractors and large employers, Southwest had not spoken out. Southwest finally told employees last week that they had to be fully vaccinated by December 8 if they want to keep their jobs. Workers may request to skip shots if they are needed for religious or medical reasons.

The Federal Aviation Administration admitted Friday’s delays in Florida, but rejected Southwest’s air traffic control explanation. Sunday’s FAA statement stated that “some airlines” were having problems due to crews and planes being out-of-position. Southwest was the only airline that reported such a high percentage of cancelled and delayed flights during the weekend.

Raymond James’ airline analyst Savanthi Syth said that the weekend problems at Southwest will cause an increase in Southwest’s costs and worsen union relations.

Southwest’s summer was difficult with high numbers of cancelled and delayed flights. It announced in August that it would reduce its September schedule by 27 flights per day (or less than 1%) and 162 flights per day (or 4.5% of the schedule) from October through November.