By Chris Isidore, CNN Business

RALEIGH-DURHAM AIRPORT – Canceled flights, packed planes, rising fares and violent outbursts are the new normal for air travel. Flying is getting worse for both passengers and crews.

The problems run deeper than the operational meltdowns that caused Southwest and American Airlines to cancel thousands of flights over four-day periods in recent weeks, each time stranding tens of thousands of angry passengers.

Staffing shortages are leading to overworked flight crews and most of the canceled flights. Vaccine mandates could lead to even more staffing shortages. Less choice in flights has led to higher ticket prices. And altercations over masks have been the cherry on the top of a miserable year for travel.

Those issues will continue well into the holiday season — and perhaps they’ll get even worse.

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American and Southwest blamed their recent service meltdowns on lacking enough pilots and flight attendants to adjust for cancellations that began with bad weather. Southwest’s October 8-11 cancellation nightmare cost it $75 million, the airline reported recently.

Officials with various airline unions say that their members are stressed to the “breaking point” by work conditions because of understaffing. Many pilots and flight attendants say they’re having trouble getting hotel rooms they need to have the government-mandated rest while working.

Pilots at American have held informational pickets in recent weeks to complain about work conditions, and Southwest pilots are planning their own pickets this month. And the airline unions say they’re worried that the problems will get worse with the pick-up in travel expected over the holidays.

“We want that flying to get done, but we don’t want tickets sold that can’t be fulfilled,” said Capt. Dennis Tajer, an American Airlines pilot and spokesman for the Allied Pilots Association, in an interview last month about the holiday season. “Are they biting off more they can they chew?”

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Worries about vaccine rules

Both American and Southwest say they will comply with federal rules set to go into effect for government contractors in early December that will require their employees to have gotten the Covid-19 vaccine.

Delta Air Lines has said it doesn’t believe it has to comply with those stricter rules, although all airlines will soon have to comply with federal demands that businesses with 100 or more employees require either a vaccine or weekly Covid tests.

Some industry analysts believe complying with those rules will mean a large number of airline employees won’t be able to work during the holiday period, or who will quit their jobs rather than comply.

Southwest CEO Gary Kelly recently said he does not believe the airline will have to fire unvaccinated employees to comply. Instead he said they will likely be accommodations allowed for employees with religious or medical reasons not to get vaccinated, possibly through the use of regular Covid testing.

“The last thing I want is our people distracted with something like this vaccine mandate [during the holidays],” he said to investors last month. “The last thing I want is for people to fear that they won’t be able to work or have a job.”

But Scott Kirby, CEO of United, which put in place toughest vaccine mandate in the industry even before the federal rules were announced, said he believes allowing airline employees to avoid vaccines through regular testing will cause problems of its own, including the airlines suddenly not having employees available to work due to testing positive or not getting back test results. He believes that United, which has had almost all employees already get vaccinated, is the only one that can promise passengers that their flights won’t be upended by Covid safety protocols.

“Imagine if you have thousands of employees on one day calling in and saying, ‘For some reason, my test didn’t pass,'” he said to investors. “I mean it is going to be a huge challenge for airlines that are not implementing vaccine requirements. Customers can book with confidence on United. We’re done with it.”

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Fewer seats, higher fares

As airlines try to hire more workers, and encourage them to be fully vaccinated, the companies are dealing with staffing issues by trimming their flight schedules.

That means fewer options for passengers booking flights, higher fares for the available seats, and packed planes. Although passenger traffic has yet to return to pre-pandemic levels, airlines have also not restored their schedules to the number or routes and planes they were flying in 2019.

In July 88% of available passenger seats were filled on domestic flights, according to the most recent data from the Transportation Department. That is the highest monthly reading since July of 2019, months ahead of the pandemic.

Data from the major airlines show that the percentage of seats sold fell somewhat in August and September as the number of Covid cases surged and the summer travel season came to an end. But the fares to book flights stayed very high throughout the quarter.

The average amount paid to fly a mile on the four major airlines in the third quarter was off only 4% from what they paid in the third quarter of 2019.

Because the two most expensive plane tickets — those purchased by business travelers and international passengers — was still only a fraction of pre-pandemic levels, that means that the leisure travelers packing into planes were paying far more they did to fly during the same period of 2019.

Fares are likely to stay high or go higher in the months ahead.

All the airlines are reporting strong bookings during the Thanksgiving and end-of-year holiday periods. And all are being hit with higher fuel prices, which typically translates into somewhat higher fares, especially at times of strong demand.

Delta recently warned that it expects to pay $1.94 a gallon for fuel in the third quarter — up 55% from a year ago but about the same price it paid two years ago. But the company warned it expects to pay between $2.25 to $2.40 a gallon on average over the last three months of the year. Fuel is the second largest cost for airlines behind pay and benefits for employees.

And Delta said after just posting its first quarterly profit since the start of the pandemic, it expects to lose money in the fourth quarter because of the higher fuel costs.

Not only will the airlines do their best to raise fares to cover higher fuel costs, they also will further trim the flights that are less profitable to limit their fuel consumption. Once again that limited supply itself leads to less choices for passengers and higher fares.

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Rising number of unruly, unhappy passengers

The fuller planes and rules about wearing masks during flights, unpopular with some passengers, just add to the tensions on board.

Airlines have reported a record number of violent clashes between flight attendants and passengers. A survey by the Association of Flight Attendants found that 85% said they have dealt with unruly passengers as passenger volumes picked up in the first half of 2021. More than half 58% experienced at least five incidents. And 17% reported a physical fight.

Last week a passenger hit an American Airlines flight attendant twice in the face, breaking her nose. Earlier this year a Southwest flight lost two front teeth and sustained facial injuries from an attack by a passenger.

There have been about 5,000 formal reports of unruly passengers so far this year, according to the Federal Aviation Administration, with 72% of them related to disputes over wearing masks. While the number of cases are down from earlier this year, before the FAA stepped up enforcement action, it is still far more frequent than pre-pandemic levels.

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