Washington — The American Civil Liberties Union (ACLU) on Tuesday said the federal government continues to "systematically" separate migrant children from their parents, accusing the Trump administration of violating a court order prohibiting officials from separating families unless in extraordinary circumstances where the children are in danger.

In a court filing in the U.S. District of Southern California, the ACLU said the administration has forcibly separated more than 900 migrant children in U.S. custody from their parents since one of the court's judges, Dana Sabraw, ordered the government to halt its controversial "zero tolerance" policy in June 2018. Along with instructing the administration to reunite all separated families, Sabraw decreed that families should not be separated "absent a determination that the parent is unfit or presents a danger to the child."

The plaintiffs in the litigation, a group of migrant families represented by the ACLU, said the administration is violating Sabraw's ruling, and asked the court to hold an in-person hearing "as soon as possible" and to issue more detailed guidance about "permissible criteria" for the government to separate families.

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"The government is systematically separating large numbers of families based on minor criminal history, highly dubious allegations of unfitness, and errors in identifying bona fide parent child relationships," the filing states.

The ACLU denounced a "concerning feature" about the recent and ongoing separations: About 20% of the cases involved children under the age of 5.

A boy and father from Honduras are taken into custody by U.S. Border Patrol agents near the U.S.-Mexico Border on June 12, 2018 near Mission, Texas. John Moore / Getty Images

In its 218-page filing, the ACLU said the administration is separating families because of minor crimes like traffic violations and fraud offenses, unsubstantiated doubts about parentage, "questionable" allegations of gang affiliation against parents, safety and space concerns in family detention facilities and other "unjustified reasons."

Some of the separations, the ACLU alleged, occurred because of allegations and arrests in the parents' records, not criminal convictions. Others were because of offenses that transpired "years ago."

In one example cited by the plaintiffs, a father was separated from his sick 1-year-old daughter after a Customs and Border Protection (CBP) officer determined he was "neglectful" for waiting until she woke up to change her diapers. In another separation, officials faulted a parent for his daughter's malnutrition, but the ACLU said her "health issues were due to her community's deep poverty, not parental neglect."

One father who faced no allegations of criminality or unfitness was separated from his three daughters because of an HIV diagnosis. Other parents, the ACLU said, were separated from their children after officials initially did not confirm lineage, but later did.

Another father named Adolfo from El Salvador was separated from his two children after the U.S. government accused him of being a gang member and of committing crimes in Honduras. But the man's attorney filed a background check that showed another person with a similar name and date of birth had a criminal history.

During an emotional encounter captured by CBS News in May, Adolfo reunited with his son and daughter after 184 days of being separated.

According to the filing, some allegations of gang allegation have "little, if any" merit, as the administration has released parents from custody when presented with evidence that the migrants were not involved with gangs. The ACLU said officials have even separated families after accusing mothers who were victims of gang violence of being gang members themselves.

"One mother was a former police officer who experienced gender-based violence at the hands of gang members; another was forced to be the girlfriend of a gang member," the filing states. "Yet another mother was brutally raped by a gang member, who forced her son to watch the assault ... One mother was in the wrong place at the wrong time — she was arrested while leaving a store near where gang members were arrested."

The plaintiffs asked the court to bar the government from separating families "without objective and concrete evidence that the parent is unfit or a danger to the child."

The 900 families cited by the ACLU were separated by the government between Sabraw's order in June 2018 and last month. Before Sabraw handed down his ruling last summer, the administration separated 2,600 migrant children from their parents or legal guardians under its "zero tolerance" policy, which President Trump was forced to rescind amid a massive public uproar.