From the Rio Grande Valley in Texas to the Southern California coast, the Trump administration continues separating migrant families at rates that alarm immigration attorneys and advocates, even though a federal judge barred family separations as a systemic policy.

Separations have slowed significantly since a federal judge in San Diego ordered the administration to halt the practice in June 2018. U.S. District Judge Dana Sabraw allowed separations in rare, specific circumstances, and the Trump administration has exploited those openings at a worrying clip, according to groups that work with migrants along the border.

"We are alarmed," said Jennifer Nagda, policy director at the Young Center for Immigrant Children’s Rights, a Chicago-based national human rights group. "In March and April, we again saw a notable increase."

Examples include:

Advocates at the Young Center's Harlingen, Texas, office said one in every five families they see at migrant shelters have been separated at the border for questionable reasons. The children ranged in age from 18 months to 15 years old.

Attorneys with the Texas Civil Rights Project said they've counted more than 40 separated families a month in the McAllen area since the injunction in June.

Officials at Al Otro Lado, which advocates for immigrants in California, said dozens of families are separated each day throughout the San Diego metro area.

The official government count is at 389 separated families since last summer's injunction, according to data received by the American Civil Liberties Union in court filings. One-fifth of the newly separated children are younger than 5 years old, according to the figures.

Advocates said that border-wide, the number of separated children is much higher.

Efrén Olivares, racial and economic justice director of the Texas Civil Rights Project, said he realizedthat the government still intended to separate children at the border days after the injunction. Sitting in the federal courtroom in McAllen, he learned of multiple cases of families being separated. One man from Guatemala had his 2-year-old-daughter taken away from him despite having a birth certificate with both their names and no prior criminal record, Olivares said. It took nearly a month to get them back together.

"We knew then we couldn’t let our guard down," Olivares said. "This was still happening every day."

Acting Homeland Security Secretary Kevin McAleenan told a congressional panel Tuesday that his department is conducting "less than two" family separations per day, which he described as minor compared with the 1,600 family units crossing the border each day.

"It's being done very carefully in extraordinarily rare circumstances," McAleenan testified before a House appropriations committee.

Officials at the Department of Homeland Security, which oversees all immigration enforcement, and U.S. Customs and Border Protection, which carries out the separations, refused to answer questions about the separations. They would not say how many separations have occurred since Sabraw's order or what happened to the separated minors.

The Department of Health and Human Services, charged with caring for the migrant children, refused to comment on the number or status of separated migrants in its custody. "HHS is not a party to the child's immigration proceedings," the department said in a statement.

The separations occur amid the shakeup at Homeland Security, which led to the departure of its chief, Kristjen Nielsen, on April 7. Trump said he wants the agency to take a firmer stance against illegal immigration as the number of Central American families requesting asylum skyrockets and holding facilities along the border overflow.

"Danger to child":Despite ban, separating migrant families at the border continues in some cases

In March, Border Patrol agents apprehended more than 92,000 immigrants illegally crossing the border, a 12-year high, including 53,077 members of family units, an all-time high.

McAleenan, Nielsen's replacement, said during an interview with NBC News that family separations are "not on the table" because the policy is "not worth it."

Border groups said those pronouncements from Washington do not reflect what they see on the ground.

'Zero tolerance' policy

Family separations ramped up in the summer of 2017 when the Trump administration started a pilot program in Texas to charge all undocumented border crossers with criminal violations, a change from previous administrations that treated first-time illegal crossings as mostly civil infractions.

Migrant parents were transferred to adult detention centers to await prosecution while their children were transferred to the care of HHS. That program was kept a secret, but in April 2018, then-Attorney General Jeff Sessions announced that “zero tolerance” would be the new policy of the Justice Department. That led to more than 2,800 family separations.

Republicans and Democrats alike called the policy inhumane and declared that the United States should not tear apart families and detain children in "cages." Facing that mounting pressure, Trump rescinded the policy in June 2018.

A week later, Sabraw issued his ruling barring the government from having a policy of separation and ordering the administration to reunite all migrant families that were separated. On April 25, Sabraw went a step further, ordering the administration to identify within six months all families that were separated under the Texas pilot program.

Family separations persist

Border Patrol agents can separate a family if they decide the adult and child are not really related or if the parent is deemed a danger to the child. The agents use everything from years-old DUIs on an immigrant's record to old theft charges as reasons to separate – not typically offenses that merit a family separation, said Lee Gelernt, an attorney with the ACLU.

"They're separating families for crimes that have no bearing on parents as a danger to the child," he said. "If there's some rhyme or reason to it, we don’t know."

In Tijuana and across the bridge in San Diego, attorney Erika Pinheiro of Al Otro Lado said she constantly meets and hears of families who have been separated because the parents have been deported – even if the children are U.S. citizens, she said. The separations happen even for asylum seekers arriving at legal ports of entry, Pinheiro said.

After being separated, adults are transferred to detention centers, often run by Immigration and Customs Enforcement, and children are transferred to shelters operated by HHS.

In September, KPBS-TV in San Diego obtained county data showing that since July, at least 54 children who were U.S. citizens were transferred to county Child Welfare Services by law enforcement agencies after being removed from asylum-seeking parents at the border, including ports of entry. Pinheiro said the overall number of separated families is much higher.

"It's devastating," she said. "These parents will never be the same; the kids will never be the same. It's such a deep trauma for them."

Olivares, of the Texas Civil Rights Project,and attorney Laura Peña, who worked with the group, released a report in February that identified 272 adults separated from a child family member, including 38 parents or legal guardians separated from their children. The youngest child was 8½ months old at the time of separation from her mother, the study said.

Separations have continued through the spring at the same pace, Olivares said. "It's so easy for a Border Patrol agent to separate a family," he said. "Then it’s a nightmare to get them back together."

Supporters of the policy say increased separations are necessary to deal with the crush of migrants arriving at the border.

Jessica Vaughn, of the Washington-based Center for Immigration Studies, a nonprofit research institute that promotes stricter controls on immigration, said Border Patrol agents have no choice but to scrutinize every parent-child pair that crosses the border and err on the side of caution.

Smugglers, knowing that migrants who cross the border with a child are often released until their asylum court hearing, send migrants with children who are often not their own, she said.

"There's an incentive for people to bring children to do this and hope that you don’t get caught bringing a child that’s not your own," Vaughn said.

According to Border Patrol data, such cases account for less than 1.2% of all families that cross the southern border.

From April 2018 through March 2019, the Border Patrol apprehended 256,821 members of family units. About 3,100 of those were cases in which the Border Patrol identified some kind of fraud – either the "child" was actually over 18 years of age or not related to the adult.

Laura Belous, advocacy director for the Florence Immigrant and Refugee Rights Project, the only legal services provider for detained migrants in Arizona, said the number of separated families dropped significantly after the injunction in June – but her office noticed a steep rise in cases again this year.

From January through April 24, her group recorded 21 cases of family separations, she said. In at least three of those cases, the parent or child was not given any reason for the separation. Attorneys are struggling to learn what the criteria are for separating families and what recourse there is for challenging those decisions, Belous said.

"It’s extremely alarming," she said. "This is a huge trauma for both the parent and the children, and really it is in violation of the law."

Bed-wetting, sleeplessness and other impacts of separations

Child welfare advocates worry about the long-term damage the separations have on the migrant children and their parents.

Officials at the Young Center, which receives federal funding to advocate for migrant children in government custody, documented cases of children who suddenly lost potty-training skills, forgot their native language, had trouble sleeping or regressed in other ways after being separated from their parents, Nagda said. Some children believed their parents willingly left them.

Another challenge is finding parent and child after they're deemed to be reunited, Nagda said. Tracking systems are different for adults and children and are not interconnected. Advocates have taken up to a year to reunite children with their parents, Nagda said.

"There's no justification for perpetrating that type of harm on a child," she said.

Immigrant parents, distraught at losing their children, fail their "credible fear" interviews because they can't focus on their case, Pinheiro said. During that interview, which is conducted by a U.S. Citizenship and Immigration Services officer and represents the first step in a lengthy legal process to win asylum, migrants must show they have a "credible fear" of being persecuted if they return to their home country.

"It's a nightmare," Pinheiro said. "The point of our asylum system is not to put lifelong trauma on people asking for protection."

Contributing: Rafael Carranza of The Arizona Republic

Follow Jervis on Twitter: @MrRJervis; Gomez: @AlanGomez; and Carranza: @RafaelCarranza.