Story has been updated with Southwest share performance and analyst opinion on Southwest.

NEW YORK ( TheStreet) -- The Transportation Security Administration is admitting that it messed up at Chicago's Midway Airport on Sunday, the busiest travel day of the year, because it opened airport security checkpoints a half hour after airline ticket counters opened.

Midway ticket counters opened Nov. 30 at 3:30 a.m., but the checkpoints did not open until 4 a.m. "Unfortunately, TSA did not open the checkpoint earlier than normal in anticipation of the increased volume, which resulted in a surge of passengers as the checkpoint opened," the agency said, in a prepared statement issued late Monday.

Some media outlets reported that lines at Midway stretched for a mile or even more. But TSA Spokesman David Castelveter said the line was under a half mile long at its worst, which involved wait times of about 50 minutes.

"TSA is currently reviewing the causes of (Sunday's) longer than usual wait times at Midway to prevent a similar occurrence in the future," he said. "Unfortunately, some passengers experienced wait times that well exceeded 20 minutes on the morning of Nov. 30, the busiest travel day of the year."

The lines cleared out by around 9:15 a.m., according to Chicago media reports.

Southwest Airlines
(LUV) - Get Report spokeswoman Emily Samuels said the airline's first flight Sunday departed at 5:25 a.m. For the TSA to open security lines at 4 a.m. on an extremely busy travel day is "cutting it pretty close," she said.

Southwest operates about 90% of the flights at Midway. Samuels said it is probable that some passengers missed flights because of the delays.

Southwest shares fell 3% on Monday, even though Bank of America Merrill Lynch analyst Glenn Engel reiterated in a report that Southwest and Spirit(SAVE) - Get Report are his top picks among the airlines. They are "the only North American mainline carriers that can boost margins without the help of fuel," Engel wrote, noting that Southwest will benefit from its new routes at Love Field.

However, Engel upgraded his rating on several airline stocks to buy on Monday: he had already rated Southwest a buy. Shares closed Monday at $40.50, up 115% for the year.

Generally, the TSA performed well on Sunday, when it screened 2.3 million passengers. Of those, 1.4% waited more than 20 minutes, 15.3% waited 10 to 19 minutes, and 83.3% waited less than 10 minutes in standard lines (as opposed to pre-check lines, where waits were generally shorter), TSA said.  

At Midway, "between Nov. 26 and Nov. 29, average wait times were below TSA's 20-minute benchmark, times similar to those across the nation for the same period," the agency said.

Sadly, in general, it is only the mistakes that people notice. 

-- Written by Ted Reed in Charlotte, N.C.

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