After Marcelo, a Guatemalan migrant, crossed the border with his 15-year-old son, Byron, in May, he was accused of lying about being the boy’s father and was sent back to Mexico, according to a complaint to government watchdogs announced on Tuesday.

His son was sent to a shelter for unaccompanied migrant children in Florida, the complaint said.

Immigration officials also "humiliated" Marcelo and threw Byron's birth certificate in the garbage, according to the complaint, which was announced Tuesday by the Women’s Refugee Commission.

Marcelo was sent back to Mexico “without ever having received any explanation or warning for the separation or his placement” in the return-to-Mexico program.

He remains separated from his son months later, as his attorneys have been trying to negotiate their reunification with the government, the complaint said.

“Marcelo is devastated and wants to be back with his son,” wrote Leah Chavla, a policy adviser with the Women’s Refugee Commission who wrote the complaint.

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The commission said Tuesday that it had filed the complaint with the Department of Homeland Security’s Offices of Inspector General and of Civil Rights and Civil Liberties on Friday, asking them to investigate cases where families have been split between the U.S. and Mexico after coming to the southern border to seek asylum.

Under the Trump administration's remain-in-Mexico policy, tens of thousands of asylum-seekers have been forced to wait in Mexico for court dates in the U.S. as their court proceedings play out.

The group said advocates have seen cases where part of an asylum-seeking family is processed and allowed into the U.S., while other members of the family are sent back to Mexico, including cases of children separated from their parents, legal guardians and caretakers.

"This administration continues separating families in really cruel ways," Chavla told NBC News, adding that sending split migrant families to Mexico made the separations "not as visible, but the effects are so very real."

The Department of Homeland Security did not respond to request for comment about the complaint.

In another case detailed in the complaint, a 20-year-old Honduran woman named Ana was separated from her 13-year-old brother, Alberto, despite having a letter and documents from their grandmother authorizing her as Alberto’s custodian, according to the complaint.

Immigration officials told Ana that the boy would be sent to live with his mother, who currently resides in the U.S., while she and her 5-year-old daughter would be sent back to Mexico.

“Ana and her daughter were sent back to Mexico despite the fact that her daughter was sick with a bad cough and a fever,” the complaint said. After Ana was unable to find a shelter, her mother was able to speak with some of her husband’s relatives in Durango, Mexico, where Ana and her daughter are staying as they wait for their hearing in October.

Earlier this month, Sen. Catherine Cortez Masto, D-Nev., told NBC News she had witnessed one such “tragic” story playing out at the border.

Cortez Masto said that during a visit to the southern border she met with asylum-seeking families in Nogales, Mexico, who have been affected by the Trump administration’s immigration policies.

Among the migrants she met was Karla, 23, an asylum-seeker from El Salvador who came to the United States in May with her two younger brothers and her 4-year-old child, she said. Karla and her family were fleeing violence in their home country after her mother was killed, Cortez Masto said.

The family went to the port of entry in Tijuana, Mexico, but Karla was separated from her brothers and sent back across the border, Cortez Masto said.

"She had no idea where they were taken," she said.

Karla eventually made her way to Nogales, nearly 500 miles away from Tijuana, and met a nun who brought her into a shelter for migrants, she said.

“They’re just horrific stories and tragic stories and she’s been waiting two months now,” Cortez Masto said.

Eventually, Karla was given a chance to speak to her brothers by phone and learned they were being held in a shelter for migrant children in Michigan.

“We need to be questioning really why — like in Karla’s case, she’s 23 years old, she’s the oldest sister — why were they separated?” the senator said. “Why aren’t we working to try to reunite them, to keep them together?”