Washington (CNN)"We had a shortage last night of beds for babies," an official at the Office of Refugee Resettlement wrote to the agency's director on November 11, 2017.
"Overall, infant placements seem to be climbing over recent weeks, and we think that's due to more separations from mothers by [Customs and Border Protection]," added Commander Jonathan White.
What White and other officials at the department didn't know was that the Trump administration had already launched a pilot program on the US-Mexico border that would eventually separate thousands of children from their parents and draw widespread scorn from around the country.
Inside the search for the parents of 545 children separated at the border
The exchange was indicative of the chaos that would ensue in the months to follow, as the Trump administration hastily implemented its controversial "zero-tolerance" policy, which called for the prosecution of all adults who illegally crossed the southern border and thereby, separated them from their children.
More than two years later, the ramifications of those early separations are still unfolding. A court filing revealed earlier this month that lawyers are still unable to reach the parents of 545 children who had been split from their families by US border officials between 2017 and 2018.
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The Democratic-led House Judiciary Committee opened up an investigation into the "zero-tolerance" policy in January 2019, calling for the three federal agencies involved -- the Department of Homeland Security, the Justice Department, and the Health and Human Services Department -- to turn over documents.
The investigation culminated into a 551-page report released Thursday that chronicles the development, and fallout, of the policy that led to the separation of thousands of families.
"Despite full knowledge that hundreds of children would likely be lost to their families forever, the Administration chose to expand the pilot program into a permanent nationwide policy," the report reads.
Texas landowners facing coronavirus pandemic and land seizures for border wall
"Causing further confusion, DHS leadership failed to provide advance notice to Customs and Border Protection (CBP) officers prior to the announcement of the nationwide policy, resulting in the chaotic and inconsistent implementation of the policy across the southwest border," it continues.
Dating back to 2017, the Trump administration had already begun to test out the policy, unbeknownst to officials at the Health and Human Services Department, which is in part charged with the care of migrant children.
CNN exclusively reported last year that hundreds of red flags were raised internally within the Trump administration about how families were being separated at the US-Mexico border.
The documents, which are also included in the committee's Thursday report, include anecdotes of children allegedly blindsided when they were taken from their parents after being apprehended at the southern border.
Parents of 545 children separated at US border still can't be found
One referral received by the DHS's Office for Civil Rights and Civil Liberties described 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."
Despite the issues that began to arise then, like challenges in reuniting those families that had been separated, the administration moved forward.
White said in congressional testimony last year that he raised concerns to senior officials about separating families apprehended at the US-Mexico border before the administration's controversial "zero tolerance" immigration policy was announced.
Confusion persists within the administration
Six days after sharing concerns about not having enough space for babies, White provided information to then-US Customs and Border Protection Commissioner Kevin McAleenan about the increase of children being referred to the Office of Refugee Resettlement, according to correspondence, dated November 17.
Two weeks later, McAleenan told White he should've noticed a recent change, adding: "We will be coordinating in advance on any future plans," according to the correspondence.
Exclusive: On family separations, one arm of the Trump administration raised hundreds of red flags to another
But since then, a slew of media reports, committee reports, and government watchdog reports have found that confusion persisted within the administration, even when then-Attorney General Jeff Sessions officially announced the "zero tolerance" policy in April 2018.
Thursday's report, for example, shows that sector-level guidance from the Border Patrol varied. Exceptions to family separation ranged from none, to a case-by-case basis, to leaving one adult with children 4 or younger.
"These documents show that the implementation of the family separation policy was inconsistent and disorganized, resulting in significant confusion," the report says.
The reunification process was similarly disorienting. After the policy was ended, Matt Albence, a senior official at Immigration and Customs Enforcement at the time, expressed confusion over the lack of information linking children to parents in an email to HHS.
Tom Fitzgerald of HHS responded: "We have a list of parent alien numbers but no way to link them to children."
Children waited for extended periods of time to reunite with family only for there to be delays or for parents not to arrive until the next day.
In one instance, previously reported by NBC, 37 migrant children who were being transported from one facility to another to be processed and reunified with parents waited in vans for several hours.
"I hope as we move forward there can be adjustments so that we don't put tender age kids in this position," read an email describing the incident.
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