Allegiant Air has been closely monitored by the FAA due to many emergency landings and aborted takeoffs. ABC interviewed a former Allegiant mechanic, who said "Dedicated steps were not being performed with maintenance manuals or even with general practices, before an aircraft is released." Many of these incidents had involved Allegiant's aging MD-80 aircraft, which as of November 2018 have been replaced by newer Airbus A320 family aircraft. 46 of the 86 aircraft have made emergency landings, all of which were on MD-80s. The average age of Allegiant's MD-80 fleet was 29 years compared to less than 13 years for its Airbus fleet.
On March 19, 2008, jetBlue added Orlando, Florida as a gateway focus city to international destinations in the Caribbean, Mexico, and South America. New international routes from Orlando International Airport include Cancún, Mexico, Bridgetown, Barbados, Bogotá, Colombia, Nassau, Bahamas, San José, Costa Rica, and Santo Domingo, Dominican Republic. In conjunction with the addition of new routes the airline will continue significant expansion of operations at Orlando International Airport including a planned 292-room lodge that will house trainees attending the existing "JetBlue University" training facility (opened in 2015).
A November 2016 analysis by the Tampa Bay Times noted that Allegiant's planes were four times more likely to have in-flight failures than other major US airlines. A 60 Minutes report by CBS News in 2018 continued to investigate the issues first raised by the Tampa Bay Times. Public records cited in the investigation found that the airline had more than 100 serious mechanical incidents between January 1, 2016 and October 31, 2017, including "mid-air engine failures, smoke and fumes in the cabin, rapid descents, flight control malfunctions, hydraulic leaks and aborted takeoffs." Other public records further revealed that Allegiant aircraft, on average, were nearly three and a half times more likely to have mid-air breakdowns than American, United, Delta, JetBlue and Spirit.
In March 2011, Allegiant took over charter service to Wendover Airport for Peppermill Casinos, Inc. to shuttle customers to Peppermill's three casinos in West Wendover, Nevada; the Montego Bay Resort, the Rainbow Wendover and the Peppermill Wendover. Allegiant based one 150-seat, MD-80 series jet aircraft in Wendover and more than 20 employees, including maintenance, flight crews and stations personnel.