Southwest Airlines canceled more than 1,800 flights this weekend, ruining thousands of customers' travel plans and stranding flight crews. The airline blamed the collapse on a mix of severe weather, air traffic control, and its own manpower shortfall.

Southwest said in a statement on Twitter Saturday that "ATC difficulties and disruptive weather have resulted in a high frequency of cancellations throughout the weekend as we attempt to recover our operation."

Meanwhile, FlightAware, a service that analyzes flight cancellations and delays, said American Airlines canceled 63 flights, or 2% of its operations, while Spirit Airlines canceled 32 flights, or 4% of its operations.

The airports in the United States seeing the most flight cancellations on Sunday are all major Southwest "hubs," even if the airline does not refer to them as such: Denver, Baltimore, Dallas Love Field, Las Vegas, and Chicago Midway.

"I understand this is extremely tough for all of you, and our customers are not pleased," Alan Kasher, executive vice president of daily flight operations, wrote in a note seen by CNBC on Sunday.

Southwest cancelled 1,018 flights and delayed 597 others on Sunday alone, according to FlightAware. The airline canceled 808 flights and delayed 1,187 others on Saturday.

The Southwest Airlines Pilots Association, which filed a motion seeking a temporary restraining order against the airline's COVID-19 vaccine mandate, issued a statement denying any involvement in the cancellations and delays.

SWAPA stated that it is aware of the operational problems that Southwest Airlines experienced Sunday as a result of a variety of factors. "With certainty, we can affirm that our Pilots are not engaged in any official or unofficial job actions," the association said in a statement.

In a tight labor market, the airline has struggled to hire new personnel. Bob Jordan, the carrier's incoming chief executive officer, told CNBC last month that the carrier is prepared to reduce flights over the spring break season if it lacks the people to sustain the business.

As a result of the lack of consistency in Southwest's operations, there was speculation on social media that employees were calling in sick. Some said it was to protest a COVID-19 vaccine mandate.