Watch "The Faces of Family Separation," a CBSN Original, on CBS, Saturday, December 28 at 10 p.m. ET.

Tampa, Florida — On Sundays, Estuardo tries to spend the entire day with his 5-year-old son, Ariel, who enjoys riding his blue push car outside their new home, located in a trailer park where dozens of other low-income immigrant families live.

In the weeks since they reunited, Ariel has become more attached to Estuardo, who said his son has changed since their forced separation.

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"He asked me why I left him. He thought and felt — in his heart — that I had left him," he told CBS News in Spanish. "But I have explained why it happened."

Estuardo, 27, and his son were not separated in the spring of 2018 during the "zero tolerance" border crackdown that the Trump administration was forced to discontinue after a massive public outcry and a ruling by a federal judge that barred officials from separating families except in limited circumstances, including when parents present a danger to the child.

Instead, U.S. border officials separated the Guatemalan father from his child this spring in one of more than 1,100 separations since June 2018.

Estuardo, 27, helps his son, Ariel, 5, ride his blue push car outside their mobile home in Tampa, Florida. Camilo Montoya-Galvez / CBS News

The American Civil Liberties Union (ACLU) has called the separations unlawful and cited Estuardo's case in a July court filing that accused the administration of exploiting loopholes in last summer's ruling to "systematically" continue separating migrant families.

In the filing, the ACLU said the administration is relying on minor crimes and even mere suspicion to justify more separations. The rationales, according to the ACLU, include traffic violations and theft offenses by the parents, unsubstantiated doubts about family ties, "questionable" allegations of gang affiliation against parents and other "unjustified reasons."

With these justifications, border officials have separated at least 1,134 migrant families in the past 17 months, according to numbers provided to the ACLU by the government Friday.

"They really scared me"

Ariel and Estuardo were separated after being apprehended by Border Patrol near Arizona's border with Mexico in May. In the July filing, the ACLU said the separation stemmed from Estuardo's speech impediment.

"We have a four-year-old boy in shelter in New York at this time because his father, who crossed the border with him, has a speech impediment and could not intelligibly answer the questions posed by CBP," the filing read.

Estuardo said the officers did not believe that Ariel was his son because he presented them with a photocopy of his son's birth certificate. The document, which was reviewed by CBS News, lists Estuardo as Ariel's biological father and includes a photograph of him.

Court filing by the ACLU on July 30.

He said one officer accused him of lying and smuggling Ariel to exploit legal protections for migrant families with children. "He said, 'I'm the boss here. You're in my country. You are not in your country. Here, I can do whatever I want. I'm going to give you 22 years in jail and we're going to send you to a judge to sentence you because you brought a stolen child who is not your son,'" Estuardo said.

Despite trying to reassure the officer that he was telling the truth and that blood tests would prove it, Estuardo said he and Ariel were separated. Once handcuffed and in a Border Patrol vehicle, he said he grew so desperate that he told the officers Ariel was his nephew. Fearing that his son would be stranded somewhere in the U.S. without any connection to family members, Estuardo said his sister in Florida was Ariel's mother.

"I didn't have any words to tell them, because they really scared me," he recalled. "I left there crying."

Customs and Border Protection (CBP) did not comment on the family's separation, but a spokesperson said agents presume migrants are part of a family "unless presented with articulable facts to the contrary."

"Facts that cast doubt on the veracity of the family unit claim may be gathered from sources such as interviews, documents, law enforcement systems, and engagement with consular officers," the spokesperson added.

Estuardo would spend more than four months in Border Patrol and Immigration and Customs Enforcement (ICE) custody in Arizona, while Ariel was transferred to the Department of Health and Human Services and taken to a shelter hundreds of miles away in New York City.

The two reunited in September after several advocacy groups, including Immigrant Families Together, Miles4Migrants and the Young Center for Immigrant Children's Rights, were able to track them down, contest their separation and pressure the government to release them.

Five-year-old Ariel spent four months in a government-overseen shelter in New York City for unaccompanied migrant minors, despite coming to the U.S. with his father, Estuardo. Camilo Montoya-Galvez / CBS News

Lee Gelernt, the lead ACLU attorney in the case, said Americans should continue to be concerned about ongoing family separations and how the administration is defending them.

"There's so much going on and it's tough for the public to focus too much on any one issue," Gelernt told CBS News. "But the kind of public outcry we saw two summers ago is what we need now, because otherwise, it's just going to go sight unseen and little babies are going to be scarred for life."

Ongoing separations and outdated phone numbers

During the border-wide "zero tolerance" policy that started in May 2018, parents who crossed the border illegally were referred for criminal prosecution, while their children were incorrectly deemed unaccompanied minors and sent to shelters across the country.

A recent report by the Department of Homeland Security Inspector General said the administration was planning to separate at least 26,000 children from their parents between May and September 2018.

Under pressure from both Democrats and Republicans, President Trump signed an executive order in late June 2018 that stated the administration was committed to maintaining "family unity." Six days later, Judge Dana Sabraw of the U.S. District Court in San Diego issued a ruling barring the practice unless the parents presented a danger to the child or if there were doubts they were the parents.

A footnote from the June 2018 court ruling that ordered the government to only separate migrant families in limited circumstances.

Sabraw also ordered the reunifications of most families. As of December, 2,791 of the 2,814 migrant children identified as eligible for reunification have been released from U.S. custody. Most have been reunited with parents or sponsors through efforts by an ACLU-led committee that has been tracking down separated families.

More recently, the court has also ordered the government to allow nearly a dozen separated parents who were deported to come back to the U.S. and reunite with their children. But Gelernt said the administration has yet to provide a pathway for them to do so. He lamented that only a small group of parents who were deported without their children have been granted this relief.

"Unfortunately, it's only 11 at this point," Gelernt said. "We hope that it will be more. But I think we're talking about maybe thousands of parents who are sitting in Central America without their children."

In addition to the approximately 2,800 parents unlawfully separated during "zero tolerance," 1,556 migrant children — including 204 under the age of 5 — were separated between July 2017 and June 2018, according to government figures.

The ACLU does not know how many of these children have been reunited and has faced difficulty trying to reach the parents of more than 680 of them. "What we're finding out is that the phone numbers that the government gave us are not workable or stale," Gelernt said.

Gelernt expects the government to reveal more separations as the litigation continues because it has not yet provided the number of migrant children separated between Mr. Trump's inauguration and July 2017.

The separations that have taken place since last summer are another pressing concern for the ACLU.

"When we heard that there were these many separations — close to 1,100 — we assumed that they would be all for very serious offenses in which the parent presented an ongoing danger to their child," Gelernt said. "What we've learned is that so many of them were for minor crimes, even DUIs, disorderly conduct, theft from decades ago, non-violent thefts."

A CBP spokesperson said the agency is complying with Sawbraw's ruling and that separations only occur to "ensure the safety of the child." Separations are carried out, the spokesperson added, when the parent or legal guardian poses a danger to the child, has a "criminal history" or "outstanding criminal warrant," a communicable disease, makes a "fraudulent" parentage claim or engages in criminal activity, such as smuggling, related to their entry into the U.S.

The Trump administration has told the district court in San Diego that it won't separate families if the parent has a non-violent misdemeanor and that it will exercise discretion in other circumstances. But the ACLU believes the authority the government has to separate families is still overly broad and has asked the court to set up a more rigorous process to determine whether parents pose a danger to their child — something the administration has opposed.

In a recent filing, the administration said the ACLU's suggested process represented an "unworkable, individualized, messy approach," maintaining that immigration officers "often make determinations regarding a parent and child in a quick time frame, and often based on the limited information available to them at the time of encounter."

But the ACLU has argued that child welfare experts should be making decisions about family separations, not law enforcement officers like Border Patrol agents.

"If a parent is genuinely a danger to their child, we of course want the child separated," Gelernt said. "But what we're finding out is that the government has this approach of categorically separating based on even the most minor criminal offenses."

Some of the ongoing separations since last summer that the ACLU believes were unlawful don't involve parents with criminal records. Estuardo, the Guatemalan father, did not have a criminal record, according to an ICE document reviewed by CBS News. But he was still separated from his son.

"I started crying"

While in U.S. immigration custody, Estuardo spoke three times with Ariel over the phone. Each call, he said, contained both relief and pain.

A former coffee farmer who decided to journey north after being threatened by a gang he refused to join, Estuardo knew little about the U.S. detention system or how to get out of it. At one point while detained, he became convinced that he might not see his son again.

But as he spent numerous nights at a detention center in southern Arizona, a group of advocates and lawyers were busy trying to reunite him with his son. Advocates at the Young Center for Immigrant Children's Rights, a group that works with the government to look out for the safety and well-being of unaccompanied migrant children in U.S. custody, had been assigned to help Ariel while he was at the shelter in New York City.

After learning more about the circumstances of the family's separation, the advocates came to believe it had been unlawful. They notified both HHS, which had custody of Ariel at the time, and the ACLU.

In early September, ICE granted Estuardo parole, allowing him to continue his immigration proceedings outside of detention for at least one year. He was finally free, but still about 2,000 miles away from Ariel.

With the help of the groups Miles4Migrants and Immigrant Families Together, Estuardo flew to New York. Two days after his release, Courtney Sullivan, a volunteer at Immigrant Families Together, accompanied him to the shelter in Harlem and witnessed the reunification. "The poor dad just burst into tears the second the little boy was brought in," she said.

Estuardo also recalled being relieved. "When they gave him back to me, I started crying because they had separated me from him for four months and 15 days."

Ariel appeared somewhat confused during the reunification, Sullivan said. But by the time the three had lunch at a McDonald's in Queens, the young boy was embracing his father and playing with the toy that came with his Happy Meal.

Estuardo, 27, and Ariel, 5, have their first meal together in the U.S. since their four-month separation. Courtesy of Courtney Sullivan

"It is absolutely still happening"

Gelernt, the ACLU attorney, said his group expects the administration to disclose even more separations in the coming months. Advocates at the Young Center for Immigrant Children's Rights have received about 200 referrals since last summer to help separated children.

"It is absolutely still happening," said Jennifer Nagda, the group's policy director. "In some of our offices, we have wait lists of kids who have been separated and who are waiting to get child advocates appointed to fight for them."

For Gelernt, the "zero tolerance" policy and subsequent family separations form "one of the most shameful periods in our immigration history — or maybe just generally, our history."

"I've been at the ACLU for more than 25 years, this is the worst practice that I have ever seen," Gelernt said. "I mean, we are talking about deliberately inflicting harm on little children, even babies. Using them as pawns in a larger political fight."

Ariel, 5, is set to start kindergarten later this year. Camilo Montoya-Galvez / CBS News

Although he's not well-versed in the political debate over immigration in his new home, Estuardo agreed. Separating families for no apparent reason, he said, is not fair.

"I don't want that to happen to other families, like it happened to me, because it is painful for the entire family," he said.