American Airlines flights resumed at 5 p.m. ET after a nationwide glitch in its reservations system prompted the carrier to ground all flights on Tuesday. However, even after bringing the system back online, the airline expected delays and cancellations to continue throughout the day.

"We do have redundancies in our systems," American Airlines CEO Tom Horton said in a video the airline posted to YouTube, "but unfortunately in this case we had a software issue that impacted both our primary and backup systems."

There is "no evidence that today's technical outage is related to the tragic events in Boston," said American Airlines spokesperson Mary Frances Fagan.

But the Boston blasts immediately crossed the minds of some passengers when they heard the news. “It seemed like a strange coincidence and when they said it’s nationwide, I looked at the people next to me and I said, 'I wonder if this is purposeful,"Lisa Montanaro, flying from Sacramento, Calif., to New Orleans Tuesday afternoon told NBC News.

Restaurant manager Ryan Pickett found out about the ground stop at McCarran International Airport in Las Vegas while having lunch and waiting for his American Airlines flight to Boston.

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“I went to speak with someone who was in line and they knew less than I did. It wasn’t for another 45 minutes that the ticket counter agents actually got on the PA and said something," said Pickett.

There were huge lines at every gate, with travelers frantically trying to make alternate arrangements, he said.

Pickett was rebooked on a JetBlue flight to Boston, which required him to go down to baggage claim, pick up his bags and transfer to another terminal, he said.

“I don’t think American has done very well in communicating, at least in our terminal, what the process is, how to handle it and taking care of us,” Pickett said.

American Airlines “seem a little in shock," said Montanaro. "They seem like they’re not sure what to do."

Passengers already at the airport can rebook on another airline by visiting an American Airlines ticket counter or by going to another ticket counter with their electronic ticket number. The airline said it would honor the fare difference for passengers choosing to still travel today either by rebooking through American Airlines reservations or through another carrier. For those opting not to travel today, full refunds will be issued, or reservation change fees will be waived, the airline said.

Following the ground delay, significant to excessive delays began to appear at Chicago's O'Hare International, LaGuardia, Dallas/Fort Worth International and Miami International, according to Flightstats.

Passengers took to Twitter to vent their frustrations with delays experienced while getting on flights and with take off once the plane had left the gate.

Earlier, the airline tweeted, "Our reservation & booking tool Sabre is offline."

Later, Sabre tweeted, "All Sabre systems are up and running - no issues here."

American Airlines then tweeted, "Clarification: The issue is w/ our ability to access our res system & not w/ @SabreNews. We apologize to Sabre & customers for confusion."

NBC News contributorA. Pawlowski contributed to this report.