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(CNN) —  

Hundreds of red flags were raised internally within the Trump administration about how families were being separated at the US-Mexico border, including some from months before the controversial “zero tolerance” policy was announced, according to documents reviewed by CNN.

The documents include anecdotes of children allegedly blindsided when they were separated from their parents after being apprehended at the southern border. One referral received by the Department of Homeland Security’s Office for Civil Rights and Civil Liberties describes a 14-year-old who said he was separated from his father in May 2018 “after a meal break while in custody, and was told by officers that his father would be deported.”

In another, an 11-year-old stated that he “was called aside by an officer and then he did not see his father again.” A 10-year-old with “poor communication skills” was allegedly separated from his mother in June 2018.

Taken together, the documents provide a rare glimpse into how one part of the Trump administration – the Department of Health and Human Services – was flagging cases of concern to another part – the Department of Homeland Security – during a tumultuous time that eventually resulted in the separation of thousands of families apprehended at the southern border.

HHS’ Office of Refugee Resettlement, which is charged with the care of unaccompanied migrant children, instructed staff to submit significant incident reports for alleged cases of family separation once the agency started seeing an uptick in cases, according to the agency.

The refugee agency was unaware of the “zero tolerance” separation policy prior to its public announcement in April 2018, and the reports were submitted as incidents of abuse in Homeland Security custody and sent to DHS’ Office of Civil Rights and Civil Liberties, an agency official said. The zero tolerance policy was officially implemented in May and ended in June after a public outcry.

A separation would typically occur under the pretense that there was a significant incident with a family member, such as abuse or neglect, that would prompt an incident report.

The procedure continued during zero tolerance. The civil rights office receives regular referrals from the refugee office on any complaint that might result from any process within Homeland Security, the refugee official said.

The DHS’ civil rights office, which received the referrals, “reviews and investigates civil rights and civil liberties complaints filed by the public” regarding the department’s policies and activities.

850 referrals

Of the 850 referrals to the civil rights office of family separation between January 2018 and June 2018, the overwhelming majority are from HHS’ Office of Refugee Resettlement. Others are from immigrant advocacy groups.

Twelve children who were 1-year-old or younger were allegedly separated between December 2017 and May 2018, according to the documents.

More than 100 referrals sent to DHS’ civil rights office predate the announcement of the controversial policy, according to the documents. Some cite criminal history or prior immigration violations of the parents or guardians.

There is a long-standing policy that allows immigration officials to separate a child from a parent if there are concerns for the child’s welfare.

Other referrals included in the documents are hazier. In February 2018, for example, the Office of Civil Rights and Civil Liberties received email correspondence from an individual on behalf of a 13-year-old who was also allegedly separated from his mother in December 2017, though the basis of the separation was unclear.

House Judiciary Committee Chairman Jerry Nadler cited the documents detailing alleged family separations that were obtained by the committee during a panel hearing.

“These documents are startling,” he said.

“Even more surprising, the 12 children under the age of 1, nine of those separations occurred before the Trump administration enacted the zero tolerance policy. In many cases, family separation happened without warning and without giving the children the chance to say goodbye to their families. Many were not told where their families were being taken,” the New York Democrat added.

The referrals do not explain how a case was resolved.

Watchdog reports

Administration watchdog reports have identified numerous problems in how agencies were monitoring and handling family separations.

In the summer of 2017, Office of Refugee Resettlement staff noticed a spike in the proportion of separated children relative to other unaccompanied children, according to a Health and Human Services inspector general report released in January.

Staff at the refugee agency developed mechanisms to track separations due to operational concerns, according to the report. Younger children, for example, require placement in specially licensed facilities.

Homeland Security had previously said that separations continue to take place in cases when the parents have a criminal history or medical concerns. The department, however, was inconsistent in explaining how many children were separated or what happened to them, according to the report.

“In some cases DHS has provided HHS with limited information about the reasons for these separations,” said Ann Maxwell, Assistant Inspector General for Evaluation and Inspections, in January.

“More children over a longer period of time were separated by immigration authorities and were referred to HHS for care than is commonly discussed in the public debate,” Maxwell said. “How many more children were separated is unknown.”

Last October, a Homeland Security inspector general report also found that the department was “not fully prepared” for the rollout of the Trump administration’s “zero tolerance” policy at the US-Mexico border and that it provided “inconsistent information,” which led some parents to not understand that they would be separated from their children and unable to communicate with them.

Court orders in an ongoing lawsuit over family separations have forced officials to identify and reunify a majority of those separated.

During a House Oversight Committee hearing last week, Acting Homeland Security Secretary Kevin McAleenan said he would “go back and redo” the zero-tolerance policy if he could, saying the policy played a role in the department losing the public’s trust.

McAleenan also said fewer than 1,000 children have been separated from their parents at the southern border this fiscal year. The department has also warned of individuals posing as families to gain entry into the US.

This story has been updated.