Washington (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.

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