The incident, which took place on a flight from San Francisco to Washington last week, reflects a growing problem for the airline industry.
Complaints by disabled passengers over civil rights violations are on pace this year to surpass complaint totals for each of the last six years, according to data from the U.S. Department of Transportation.
In the latest incident, D'Arcee Neal, who has cerebral palsy, reportedly crawled out of his seat when his United Airlines flight landed in Washington because a special wheelchair that fits in the aisle was not immediately available.
In a statement, United acknowledged the airline made "a mistake" by taking away a wheelchair that was arranged for the 29-year-old passenger, who said he couldn't wait because he needed to immediately use a restroom.
"We've apologized to him for that delay," the airline said. "We hope that all of our customers understand that this situation doesn't reflect the level of service we provide to customers with disabilities each day."
The airline, which offered Neal $300 in compensation for the incident, said it operates a "24-hour Disability Desk" to assist passengers with disabilities.
But complaints against airlines over the treatment of passengers with disabilities have been on the rise.
Last year, 774 complaints were filed by disabled passengers with the U.S. Department of Transportation over civil rights violations, up 50% from the 519 complaints filed in 2009.
In the first six months of 2015, 459 complaints have been filed over civil rights violations of disabled passengers, putting the U.S. airline industry on pace to surpass last year's total by 18%, according to data from the U.S. Department of Transportation.
A 2014 analysis of citations against airlines by the Los Angeles Times, found that the U.S. Department of Transportation imposed the steepest penalties against airlines that mistreated disabled passengers.
"There are good examples of the airline industry making progress in the area of serving customers with disabilities -- but more work remains to be done," said Brandon M. Macsata, general consultant for the National Business & Disability Council at the nonprofit Viscardi Center. "Unfortunately, there are too many stories of egregious treatment of customers with disabilities flying on domestic, as well as international air carriers."
To read more about travel, tourism and the airline industry, follow me on Twitter at @hugomartin.