MIAMI (CBSMiami) – Travel troubles for some passengers flying Southwest Airlines.

They searching for a way to get to their destination after nearly 2,000 flights were canceled over the weekend.

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Monday morning, most of Southwest’s flights out of Miami International Airport were scheduled as “on time.”

A Southwest passenger and his fiancé who are trying to get back home to Chicago said they found out Sunday their flight was canceled.

“We stayed on the phone for five hours and couldn’t get through to Southwest. We came up here yesterday and waited in line for about two hours just to be told that hey, they weren’t going to do anything but give us an $80 voucher for a room,” he said.

Another passenger said she too had to spend an extra night in Miami.

“We spent the night here in the airport hotel,” said Amber Muir.

Muir and her son are trying for a second time to head home to Denver, after a weekend of baseball in Miami.

Their flight Sunday on Southwest was canceled.

“We were supposed to be boarding and they said they were waiting on a flight attendant, so we were delayed an hour, and then next thing I knew I got a text that it was canceled,” she said.

Fort Lauderdale-Hollywood International Airport said they are also experiencing some Southwest flight disruptions due to lingering operational issues from the weekend. They urge passengers to check with the airline before heading to the airport.

At Miami International, Southwest had four arrivals and three departures canceled as of Monday morning. At Fort Lauderdale-Hollywood International, Southwest canceled 12 arrivals and 12 departures.

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The airline canceled more than 1,000 flights in total, or 29 percent of its schedule on Sunday, according to flight tracker FlightAware. That was the highest rate by far of the major U.S. airlines. On Saturday, Southwest Airlines canceled more than 800 flights.

Southwest says air traffic control and weather-related challenges caused the cancellations but the FAA responded Sunday saying its staffing shortages ended Friday and that airlines are having “challenges due to aircraft and crews being out of place.”

“What really bothers me is Southwest is trying to blame the FAA air traffic control system. It’s like saying the dog ate my homework,” said Henry H. Harteveldt, president and travel industry analyst at The Atmosphere Research Group.

Southwest is reportedly clashing with its pilot’s union over the federal vaccine mandate.

The Southwest Airlines Pilots Association filed a lawsuit on Friday but denies it organized a so-called “sick-out” and says there were many operational difficulties due to management’s poor planning. Southwest says it’s operating at lower staff levels than it did pre-pandemic and cannot recover quickly.

Sources told CBS News a staffing shortage this weekend was a factor in why so many Southwest flights were cut.

So what is the connection between the union lawsuit we saw filed on Friday and the cancellations?

“Officially, there’s no connection. Unofficially, what I’ve heard is there are some rogue pilots who are anti-vaccine folks. They are not showing up for work,” said Harteveldt.

“Southwest’s absolute meltdown doesn’t bode well for Thanksgiving or for Christmas,” he added.

Internally, Southwest is apologizing to displaced staff who couldn’t find hotels or accommodations which only added to the scheduling issues and cancellations.

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The federal vaccine mandate for airlines hits December 8 and Southwest’s pilot’s union says it is considering an official demonstration also in December.

CBSMiami.com Team