Frustrations for flyers are sky-high with thousands of flights cancelled across the country, many of which coming from Southwest Airlines – now the focus of a federal investigation from the U.S. Department of Transportation.

The federal agency is looking into whether the cancellations were controllable and if the airlines is complying with its customer service plan.

Southwest says the massive winter storm impacted two of its biggest hubs in Chicago and Denver. The CEO claims the company's outdated scheduling software made it a challenge to regroup from those cancellations once the storm subsided.

According to Flightaware.com, over 3,000 flights were canceled just Tuesday. Over 2,500 of those were Southwest flights.

Customers, some of whom were left stranded on Long Island, are now scrambling to figure out how to get back home.

Regina Herman came to visit family in Holtsville from her home in Myrtle Beach, South Carolina.

She says her flight on Christmas Day was delayed for hours and she ended up spending five hours in the Baltimore airport before finally making it to Long Island later that night.

Now she is hoping to head back home on Wednesday.

"Every flight has been canceled but there is one that I am booked on tomorrow evening at 5:30 p.m. and nobody can tell me if it's a go or not," Herman said.

Zhiao Zhang was supposed to fly into LaGuardia on Christmas Eve and says Southwest canceled his flight an hour before take-off. He says they then rebooked him and his family to Dec. 27.

Zhang says he has been trying to get back home for days and ended up at MacArthur Airport to get his luggage because it was one of two airports his flight was rerouted to.

"This is not fair at all...and this is clearly an operational problem," Zhang said.

Southwest is warning the cancellations and delays are expected to continue for several more days.

Aviation expert Michael Candors, of Farmingdale State College, says Southwest uses a point-to-point system, instead of a hub system, which could be causing some of the extra delays and cancellations.

"The advantage of the hub is the opportunity to respond to contingencies because you have a lot of airplanes and you have a lot of pilots at the hub," Candors said.

Candors said that Southwest's system could have planes that get stuck in other parts of the country.

According to their website, those who have flights canceled can request a full refund or get a flight credit. It also says they could submit receipts for what they had to spend on meals, hotels, rental cars or train tickets because of their canceled flight.

The airline says it honors reasonable requests for reimbursement.

Southwest's website also says hold times on their phone line average are over two hours and have been as long as four.

The company encourages customers to use its app.

The company's CEO Bob Jordan apologized late Tuesday.

"We're doing everything we can to return to a normal operation and please also hear that I'm truly sorry," Jordan said.