New York (CNN Business) – The long weekend dragged on for Southwest customers after the airline canceled more than 1,000 flights on Sunday. That is about 27% of your daily operations. It’s the second day of massive cancellations by the world’s largest low-cost airline.

The company blamed the cancellations on air traffic control problems and limited personnel in Florida, as well as bad weather.

“We continue to work diligently throughout the weekend to reestablish our operation with a focus on repositioning aircraft and crews to take care of our customers,” the airline said in a statement Sunday.

In a statement, the Federal Aviation Administration (FAA) said there have been no cancellations related to air traffic since Friday. The agency said airlines are experiencing delays due to planes and crews being misplaced.

“Flight delays and cancellations occurred for a few hours Friday afternoon due to widespread severe weather, military training and limited personnel in an area of ​​the Jacksonville Air Route Traffic Control Center,” the FAA said.

However, other airlines did not appear to be as affected by these problems. On Sunday, American Airlines canceled 2% of its flights and the low-budget Spirit Airlines also canceled 2%, according to FlightAware.

It was a very busy travel weekend since Monday is a federal holiday. Southwest canceled 808 flights on Saturday, stranding thousands of passengers across the country.

Marye Cory was scheduled to fly from Oklahoma City to Orlando on Sunday morning for a cruise. At 3 a.m., he saw that his flight had been canceled and he spent more than eight hours on the phone with customer service.

Cory said he spent more than $ 400 and used 20,000 credit card points on a United flight leaving the morning of his cruise. He also lost money on a booked AirBnb in Orlando and had to reorganize childcare.

“I have flown with Southwest over 200 times and have always been very happy with their customer service,” said Cory. “I hope they fix this.”

Last week, the airline announced a vaccine mandate for employees, fueling speculation that the weekend’s delays may have been caused by the departure of a pilot.

“Southwest Airlines must join with our industry peers to comply with the federal government’s covid-19 vaccination directive,” said Gary Kelly, president and CEO of Southwest Airlines in a statement. “I encourage all Southwest employees to comply with the federal directive as quickly as possible, as we value each individual and want to ensure job security for everyone.”

The Southwest Airlines Pilots Association (SWAPA) said the cancellations were due to “poor management planning.” CNN has reached out to SWAPA for comment.

“SWAPA is aware of the 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 labor action,” the union said in a statement.

Southwest has had a difficult year. The airline had the worst punctuality performance and the highest percentage of canceled flights from any of the country’s four major airlines in June and July, according to flight tracking service Cirium. Passengers aren’t the only ones upset with Southwest: Pilot, flight attendant and mechanic unions have voiced complaints about the airline’s operations.

Southwest promised to address the problems by scheduling fewer flights in the fall.

“To any Southwest customer whose trip with us did not meet their expectations this summer, we offer our sincerest apologies,” Kelly said in a statement. “We are confident that these adjustments will create a more reliable travel experience.”

The airline said the modified schedule affected operations this weekend.

“With fewer frequencies between cities on our current schedule, recovery during operational challenges is more difficult and lengthy,” Southwest said in a statement.

– CNN’s Chris Isidore contributed to this report.

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