The federal government has fined Delta Air Lines $50,000 in civil penalties over two incidents where airline employees allegedly discriminated against Muslim passengers.

The incidents happened in 2016, including one on a flight from Amsterdam's Schiphol Airport to Kennedy Airport. Passengers on Flight 49 on July 31, 2016 reported to the flight crew that a man called Mr. A, "a Muslim passenger," was "making 'significant eye contact' and later speaking with a person of similar ethnicity in the gate area. The passengers observed that the person to whom Mr. A was speaking did not board the flight but appeared to give Mr. A a small package," according to the consent order issued by the federal Department of Transportation on Friday.

"The flight attendants observed Mr. A on board the aircraft and he moved from a non-window seat to a window seat, looked outside the window constantly, and appeared to be perspiring. The flight attendants shared the other passengers’ and their own observations with the Captain of Flight 49. At the Captain’s request, the First Officer then walked through the cabin but observed nothing remarkable about Mr. A. After some inquiry, Delta Corporate Security informed the Captain that Mr. A’s record had “no red flags," the order continues. "The Captain decided to proceed with the flight with Mr. A on board and pulled away from the gate; however, the Captain changed his mind after the flight attendants expressed, without any intervening incident, that they remained uncomfortable. The Captain returned to the gate and requested that Mr. A be removed and booked on a later flight."

The DOT said the rebooking happened without further additional security screening and didn't follow Delta's own security protocols, showing the airline staff's removal of the passenger was "discriminatory."

"This action was taken without following required Delta security protocol. Moreover, even though security inspected the area surrounding Mr. A’s seat and his baggage was offloaded, Mr. A was not subjected to additional security screening prior to being rebooked. Therefore, we find that the Captain’s removal of Mr. A on Flight 49, on July 31, 2016, from Amsterdam to New York after being cleared was discriminatory," the order said.

The DOT order noted that "although an airline has the legal authority to refuse to transport an individual that it decides is unsafe, Federal law prohibits any airline decision to refuse to transport that is based on the person’s race, color, national origin, religion, ethnicity, or sex."

A representative for Delta said in a statement the airline's goal is "to model inclusion."

"We are built on a culture that treats all customers - regardless of race, ethnicity, or religious affiliation - with dignity and respect," said Lisa Hanna, a spokesperson for the airline. "Unlawful discrimination of any kind is not tolerated. Our commitment in this area is unwavering. While we understand that our best customer service was not reflected in how the incident was handled, we disagree with the Department of Transportation's contention that Delta engaged in discriminatory conduct. For that reason, we have worked to improve our investigative process since these incidents and we have supporting programs, policies, training and procedures that back up our commitments in this area.”

The other 2016 incident involved a married couple, called Mr. and Mrs. X in the DOT order, who were traveling from Paris to their hometown of Cincinnati. On Delta Flight 229 on July 26th, 2016, Mrs. X wore a headscarf and Mr. X allegedly fiddled with his watch, which made another passenger suspicious and complained to a flight attendant.

"The flight attendant stated that as she walked through the cabin on a routine task, she observed Mr. X texting on his cell phone using the word 'Allah' several times. As the flight attendant approached Mr. X, the flight attendant reports that Mr. X made eye contact with her but did not smile and reached over to pat his wife’s hand. The flight attendant then informed the Captain of the passenger’s account and her observations. In the meantime, another flight attendant walked through the cabin and observed Mr. X texting on his phone and as she passed, he changed his screen. After speaking with the flight attendants, the Captain conferred with Delta’s Corporate Security, who informed the Captain that Mr. and Mrs. X were U.S. citizens, returning home, and that there were “no red flags," the DOT order said.

Mr. and Mrs. X were nonetheless kicked off the flight and interviewed by security where they appeared to have "more of a stressed (attitude) and incomprehension on their part.”

The original flight crew said they were uncomfortable having them onboard and the couple were rebooked on a different Delta flight leaving the next day -- again, in violation of Delta's own security protocol.

"It appears that but for Mr. and Mrs. X’s perceived religion, Delta would not have removed or denied them re-boarding from Flight 229 on July 26, 2016," the DOT said.

In addition to the $50,000 fine, Delta, which reported $6.2 billion in pre-tax profit last year, was also ordered to provide further civil rights and cultural sensitivity training to the flight and cabin crew members and all customer service employees who were involved.