Some of those affected were here in the Bay Area.
"Didn't think our flight was going to be canceled. We arrived, flight was canceled so we had to spend the evening here in San Francisco," said Southwest passenger Chris Vahle.
Southwest says the issues stem from bad weather and air traffic control issues.
RELATED: Southwest cancels over 1,000 flights Sunday, says issues in Florida triggered nationwide disruptions
They tell ABC7 News in a statement, "We experienced weather challenges in our Florida airports at the beginning of the weekend, challenges that were compounded by unexpected air traffic control issues in the same region, triggering delays and prompting significant cancellations for us beginning Friday evening."
But the FAA has denied any current issues, saying there have been no major air traffic control issues since Friday.
Despite the crazy weekend for many Southwest passengers, other airlines haven't experienced issues to the same extent.
On Sunday alone, Southwest canceled over a quarter of all their scheduled flights. That compares to less than 2% by competitor American Airlines.
In a separate statement issued Sunday, the union representing Southwest pilots denied the issues were caused by the company's recent vaccine mandate- rumors of which have been circulating online.
They said, "There are false claims of job actions by Southwest pilots currently gaining traction on social media and making their way into mainstream news. I can say with certainty that there are no work slowdowns or sickouts either related to the recent mandatory vaccine mandate or otherwise."
Following a morning of issues, as of Sunday evening, Southwest flights flying out of Oakland airport were operating almost as normal.
And the airline says it's working diligently to address remaining problems.
But that's still little comfort for some travelers, like Demitri Samaha.
"It'd be nice if they answered the phone or, at least, you know, try to get you another flight," he said.