ROCHESTER, N.Y. — Mercedes Phelan was confused last April when Border Patrol agents boarded the Greyhound bus she was riding in Pennsylvania and asked her if she was a citizen.

Ten months later, when she says they asked the same thing on an Amtrak train in Syracuse, N.Y., she was mad.

"I was super angry because [they were] obviously profiling," said Phelan, who is black, Puerto Rican and a United States citizen. "They literally skipped over every single white person."

She says she watched agents walk down the aisles, stopping only when they saw a person of color, to ask: "Are you from here? Do you have papers?"

Bus and train travelers across the northern U.S. report being stopped, questioned and detained with increasing frequency since the first year of the Trump administration. That year, Customs and Border Protection (CBP), the agency that oversees the Border Patrol, reversed an Obama-era decision to restrict approval for those operations.

In November 2017, according to emails obtained exclusively by the ACLU of Maine through a public records lawsuit and provided to NBC News, a Border Patrol official in Maine told agents they were ready to begin boarding buses and wished them "Happy hunting!"

Mercedes Phelan was questioned about her citizenship by Border Patrol agents twice while a passenger on Greyhound and Amtrak vehicles. Adiel Kaplan / NBC News

As the Trump administration ramps up immigration enforcement on the southern border, advocates have called attention to this quieter crackdown near the Canadian border, arguing the searches are unconstitutional. Under the Fourth Amendment, passengers cannot be detained and questioned by Border Patrol without reasonable suspicion that they are deportable, say the ACLU and allied legal groups, and that suspicion cannot be based on someone's skin color or ability to speak English.

"Customers are exposed, especially people of color, to discriminatory enforcement when the buses are boarded," said Chris Rickerd, senior policy counsel for the ACLU. "CBP has a real burden to show that these are a wise use of resources."

The searches can happen as often as three times a day at some northern bus stations, according to advocates — even those with no direct routes to the border. They have caused bus delays and missed connections and resulted in the long-term detention of immigrants allegedly apprehended through racial profiling, a violation of the Fourth Amendment and Department of Homeland Security policy.

Under immigration law, agents have the authority to search vehicles without a warrant "within a reasonable distance from any external boundary of the United States," which CBP interprets as within 100 miles of any land or water border, north or south. That massive zone encompasses areas that hold more than half of the U.S. population, including all of New England and Florida and most of New York state.

Meanwhile, according to several former Department of Homeland Security officials, the northern border is well staffed but quiet compared to the Mexican border. There isn't always a lot for agents to do. It is along the northern border where the bulk of the board and search incidents have occurred since the change in policy, say advocates and a spokesperson for Greyhound, the nation's largest bus company.

Both Greyhound and former DHS officials have criticized the practice, with the bus line expressing frustration about it to Congress. But Border Patrol views its ability to board trains, buses and other transport dozens of miles from the border as crucial in its fight against smuggling and terrorism.

CBP says the practice is lawful and denies any accusations of racial profiling. The agency is "committed to the fair, impartial and respectful treatment of all members of the trade and traveling public, and has memorialized its commitment to nondiscrimination in existing policies," a spokesperson told NBC News.

'An excellent opportunity'

Called "transportation checks" by Border Patrol agents, bus and train searches are not new. Such checks once made up a large part of agents' daily activities in some northern border sectors. But the practice has been a subject of dispute for years, with the ACLU and activists calling the checks unlawful racial profiling as far back as 2011.

Policies imposed during the Obama administration from 2010 to 2012 restricted when the checks could occur, requiring clear intelligence about smuggling or other criminal activity and approval from Border Patrol headquarters. But when the Trump administration dropped the headquarters requirement, the news was met with enthusiasm from some agents.

Border patrol agents speak with local law enforcement outside the Syracuse bus station on May 9, 2019. Adiel Kaplan / NBC News

Agents in at least one border sector greeted the 2017 change eagerly, according to emails obtained by the ACLU of Maine.

"This is an excellent opportunity, the likes of which we have not seen in a decade," a Border Patrol official wrote to a group of supervisors in the Houlton sector, which covers the state of Maine. The November 2017 email informed the agents that they were ready to begin bus checks in Bangor, Maine, 95 miles by road from the nearest Canadian border crossing.

"Remain professional, expect to be videoed, and do not get baited into an argument that will get edited to make us look like fools. Don't confuse this with taking s---," instructed the official, whose name was redacted.

The official signed off: "Happy hunting, stay safe, and have fun!"

In another email two months later in early 2018, the patrol agent in charge in Houlton, Maine, also signed off, "Happy hunting."

Click here to read the emails.

After the restrictions were relaxed, reports of Border Patrol on buses began to make headlines. According to incidents reported to advocates or described in court documents, in Florida, California, Detroit, Rochester, Spokane, Vermont and elsewhere, agents have boarded buses and asked passengers where they were born or to see their papers. Passengers filmed or photographed some of these interactions, sparking outrage online and bringing new attention to a practice that has not been so common since before the age of smartphones.

'Growing threats'

A spokesperson for CBP told NBC News checks have increased in recent years to combat the "growing threats" of transportation hubs, like bus and train stations, being used by "alien smuggling and drug trafficking organizations to move people, narcotics and contraband to interior destinations."

There is no public record of how often these checks actually lead to an arrest, and CBP said it does not breakdown apprehension data by where arrests occur. But the agency did provide arrest data for the Spokane bus stop to The Spokesman-Review in 2018, which showed that in six years, agents had arrested nearly 200 people at the bus station.

CBP does keep data on apprehensions by sector, which have increased in most of the northern border sectors since 2016. But the numbers remain low. In the sector that covers Maine, apprehensions doubled from fiscal year 2016 to 2018, up from 25 to 52 people.

Bus checks have resulted in the apprehension of people in the country illegally. But agents have also questioned citizens, green card holders and DACA recipients — in some cases detaining legal immigrants and telling them their documentation was fake.

"From an enforcement perspective, this really is a waste of resources," said John Sandweg, who served as the acting director of U.S. Immigration and Customs Enforcement during the Obama administration and worked in the DHS general counsel office when the bus checks were restricted.

"A lot of those cases that you're going to find are people who crossed the border a long time ago," Sandweg said. "They're just refielding run-of-the-mill migrants and, frankly, congesting immigration courts in the process."

Immigration court, which operates separately from the main federal court system, has long been stretched to its limits. Earlier this year, the immigration court backlog passed more than 890,000 cases, with less than 450 judges in the system to hear them.

"There was a lot of discussion of: What is the point of all of this transit enforcement and is it really border related?" recalled Margo Schlanger, who ran the DHS civil rights and civil liberties office in 2010 and 2011.

She said some of the resources at the northern border could be better used on the southern, where unprecedented border crossings and detentions threaten to overwhelm agents.

"The thing is that there is not a lot of border work to do along the northern border," Schlanger said. "There's an awful lot of sitting around."

'A reasonable person'

Mohanad Elshieky was 97 miles from the border when he said he was ordered off a bus in Spokane on a cold day in January. Elshieky, who came to the U.S. from Libya as a student but stayed after receiving death threats back home, had recently been granted asylum.

He said he had two forms of identification, which he showed to the Border Patrol agents. They were skeptical about the documentation, Elshieky recalled, telling him, "Illegals fake these all the time." The agents questioned him for nearly 20 minutes before letting him get back on the bus.

"I was honestly terrified," Elshieky said. "I've heard so many stories of people getting wrongfully detained and wrongfully deported."

Mohanad Elshieky Rose Sherman

Passenger accounts and videos show the checks follow a pattern. Agents board a bus preparing to depart, or one that has just arrived. Sometimes they have a dog, which sniffs the baggage compartment of the bus.

One agent stands at the front by the driver. Another goes to the back and begins questioning passengers. In some cases, the agents asked only people of color if they were citizens or to see their papers, passengers said. Others reported agents asking every passenger but not stopping to listen to the answers until they reached a person of color.

"When it came to Caucasian people, he wouldn't even wait for their answers," said Ava Sharifi, a student in Washington who was questioned in March 2018 and watched agents take a black man off the bus to be searched. "Once [the agent] got to a row with a person with an accent or darker skin, then he would look for answers."

Passengers told NBC News and reported to advocates or said in court documents that they often felt physically intimidated during the encounters. Elshieky described an agent leaning across his seat while questioning him after he said he was not a U.S. citizen. Phelan said the agents blocked the aisle both times she was questioned. Sharifi reported the same.

Many passengers do not know they have the right to refuse, according to advocates, and some told NBC News they felt refusal was not a realistic option.

"I did feel trapped," said a passenger who was questioned on a bus in Maine in May. She asked that her name not be used because she frequently travels internationally for work. "If I wanted to exit that bus I would have had to physically push past an officer."

"In the face of intimidating and uncomfortable interrogations, where it's unclear whether you'll get kicked off the bus if you exercise your right to remain silent, we haven't had a single person ever say they felt they were allowed to leave," said Enoka Herat, a lawyer with the ACLU of Washington.

CBP told NBC News that passengers can exit the vehicle during a bus check, and Border Patrol training materials and arrest reports paint a less intimidating picture of how checks are conducted.

In six arrest reports from a four month period in 2017, obtained through public records requests by the University of Washington Center for Human Rights, Border Patrol agents describe the process identically. Two agents boarded a bus at 5:15 p.m. on six different days. One went to the back and "began to ask each passenger as to their citizenship." The other "stayed at the front of the bus and stood near the driver's area so as to leave the aisle open to anyone who wished to freely enter or exit."

Agents "must not do or say anything that would cause a reasonable person to believe he wasn't free to end the encounter," according to a training presentation obtained by the ACLU of Maine. The presentation contains specific instructions that agents should not block the aisles or doors of vehicles they board.

The training materials also say "a bus passenger has the right to refuse consent to search and refuse to answer questions," but "the officer does not have to advise them of this right."

'Not happy'

In 2018, the ACLU launched a campaign pushing transportation companies to bar Border Patrol from entering its vehicles, arguing the warrantless questioning amounts to illegal racial profiling, and the companies have a right to refuse consent to searches.

Greyhound, which carries 16 million passengers per year, has been the main focus of the ACLU campaign. The company noted to NBC News that it is not the only bus operator that deals with Border Patrol entering vehicles and said in a 2018 letter to Congress that it "does not support or coordinate searches by CBP and is not happy about them."

Checks happen on Amtrak trains as well, though there have been fewer reports. When asked about the checks, Amtrak said via email that all passengers over 18 must carry identification and that the carrier "cooperates fully with federal authorities and federal law."

In June 2018, 23 members of Congress sent Greyhound a letter, urging the company to stop allowing Border Patrol onto its buses.

"By granting consent to CBP agents to board buses to inquire about immigration status," the representatives wrote, "Greyhound exposes its passengers to frequent violations of their constitutional rights to be free from warrantless searches and seizures, racial profiling and harassment."

Greyhound argues that its hands are tied. It is unclear if the Fourth Amendment right protecting private drivers on domestic routes from unwarranted immigration searches also applies to bus operators like Greyhound, the company said in letters to Congress and the Washington state attorney general in the last year.

"We understand the impact it has on customers and the communities we serve," a spokesperson for Greyhound said in a statement to NBC News. "We encourage those seeking changes to this practice to work with their congressional representatives to implement changes to this law."

Meanwhile, passengers have begun to sue to force change.

Elshieky, whose tweets about being questioned went viral, filed a complaint against CBP in April. He is seeking $250,000 in damages for racial profiling and unlawful detention by Border Patrol agents.

A sign in the New York Port Authority Bus Terminal informs Greyhound passengers about their rights during a Border Patrol bus check in English and Spanish. Greyhound

After being questioned on a bus in California, Rocio Cordova filed a class action suit for bus passengers against Greyhound in November. The state court case alleges Greyhound violated California civil rights and consumer protection laws by allowing Border Patrol agents on its buses.

In December, Greyhound began posting signs in its company-operated bus stations around the country in English and Spanish titled "Immigration Issues That Affect Our Passengers." A similar notice appears on the company website on a page called "Your rights and rules on board" under the heading "U.S. Customs and Border Protection Checks."

The postings include contact information for immigration legal aid groups, instructions on how to submit complaints to DHS and state that federal officials can legally board buses within 100 miles of the border without a warrant, telling riders, "Please contact your members of Congress to support changes to this law."