(CNN) Alejandra was shown her release paperwork and told she would be reunited with her 6-year-old daughter later in the day.

She was put into a separate holding facility at the Port Isabel Detention Center in Texas, where she had been separated from her daughter for weeks, and told that her wait would soon be over.

That was 11 days ago.

Alejandra is one of the hundreds of separated parents who were not reunited with their children by the Thursday deadline. Only a small number of nonreunited parents are still in government custody, though. The bulk of unreunited parents are no longer in the United States or have declined reunification with their children.

After days of limbo, Alejandra's attorney was told by the daughter's attorney that Health and Human Services (HHS), which cares for the separated immigrant children, had put a red flag on a child's case. An HHS red flag could indicate there was something that raised safety concerns for the child or questions about whether the adult was really the child's parent.

Both Alejandra and her attorney say they have not been told any specifics about the red flag.

"Please, please, I don't understand why you haven't reunited with me," Alejandra said in a phone interview with CNN from Port Isabel. "I don't know anything. You haven't told me anything. This is really strange. This is all so strange."

CNN is not using Alejandra's real name at her and her attorney's request to protect her identity and personal information.

For parents to be reunited with children by the court-ordered deadline, both Immigration and Customs Enforcement (ICE) and HHS had to clear the family for safety and parentage concerns.

HHS would not comment on specific cases, but a spokesperson said any non-reunited families are because of specific concerns.

"Parents in ICE custody that have not yet been reunited with their child are a result of concerns over safety or parentage," the spokesperson said. "(The Office of Refugee Resettlement) is working with (the Department of Homeland Security) to evaluate if a parent is eligible for reunification on a case by case basis and will continue to put the safety of children first during this process."

The American Civil Liberties Union, which brought the lawsuit that resulted in the court order to reunite separated families, has demanded more information from the government — including specific information about any parents deemed ineligible for reunification. Lead attorney Lee Gelernt has repeatedly expressed concern that the government is "unilaterally" making decisions about eligibility that the parents and their attorneys cannot challenge.

Alejandra's journey

Alejandra and her daughter attempted to enter the United States on June 9, she says, fleeing gang violence in her native Honduras. They have been separated for a month and a half. In that time, she's watched countless parents be reunited and released.

The fact that Alejandra is still waiting in Port Isabel without any information about how she will be reunited, despite ICE telling her days ago that the reunion was imminent, exemplifies the government's frenzied and hectic process as it rushes to reunify thousands of families it separated at the border. A federal judge ordered the government to reunify the families by last Thursday.

"I called my social worker Thursday and she told me that they didn't know how much longer I would be in this situation," Alejandra said.

The last time she spoke with her daughter was Thursday, according to Alejandra. The phone call lasted 10 minutes, during which she says her 6-year-old said that "she's really sad."

"My child is my whole life. Without her, I'm nothing," she said. "She's ready to be with me."

She is one of the mothers who were held at Port Isabel in an odd limbo last week, released but not yet reunited and not able to leave . Her attorney says there are more parents also in Alejandra's current position, but CNN has not yet been able to independently verify those other cases.

"[Y]ou would think that someone would tell me whether reunification was going to happen or not," Eileen Blessinger, her attorney, said.

"She was told last Wednesday that she was going to be reunited with her child. We're now at a week-and-a-half with no information. If they took the time to tell us that she's going to be reunited, you would think that they would take the time to tell us she's not going to be. Or at least give her an updated timeframe."

ICE deferred questions about Alejandra's case to HHS. ICE did not immediately respond to a follow up about why she was told she was being reunited.

ICE began processing parents that way after early in the reunion process some children ended up spending the night with adults at a detention facility not designed for families. In a statement last week, ICE spokeswoman Sarah Rodriguez said the agency changed its strategy to prioritize the children.

"In order to facilitate more efficient reunification of family units going forward, ICE has leveraged additional resources to enhance processing capacity for adults/parents held in the Port Isabel Detention Center (PIDC)," Rodriguez said. "The safety and well-being of children remains our top priority as we work to comply with the court's order as expeditiously as possible."

But Alejandra has remained in the dark.

The court case

Though the deadline had elapsed, US District Judge Dana Sabraw made clear in a Friday court hearing that more work remains to unite the families that could still be deemed eligible after the deadline.

Reflecting at a final status hearing on Friday, Sabraw noted the chaotic nature of the situation, pointing to the government's own failure at the outset of its separations to plan for reunification.

"There were three agencies, and each was like its own stovepipe. Each had its own boss, and they did not communicate," he said, according to a court transcript. "What was lost in the process was the family. The parents didn't know where the children were, and the children didn't know where the parents were. And the government didn't know either."

For her part, Alejandra called the policy that resulted in her separation "inhumane."

"I would not have come [had I known we would be separated]," "Alejandra said through tears. "I wouldn't have stayed in Honduras, I would have gone somewhere else, but I would not have come if I knew."

Correction: This story has been corrected to clarify the situation of Alejandra's paperwork for release. Alejandra was shown her paperwork, but not given the paperwork.