EL PASO, Texas -- Most of the immigrant children who'd been separated from their families and are still being held by U.S. Customs and Border Protection are expected to be reunited by the end of the day, a source with the Department of Homeland Security told CBS News.

This does not reflect the greater number of children who are in the custody of the Department of Health and Human Services. That number was reported this week to be greater than 2,340.

There will be a small number of children with Customs and Border Protection who will not be immediately reunited with their families. Reasons for delay may include if relationships can't be confirmed or if authorities think there's a risk to the child.

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At the border, the government is trying to clear up who gets prosecuted and who does not. Confusion, however, hasn't stopped border crossings, CBS News' Mireya Villarreal reports.

Video captures the moment four people tried to illegally cross into the U.S. through a canal system in El Paso. Agents pulled them to safety.

"It may look calm on the surface. The undercurrents are very dangerous," one agent said.

These cases will end up at courthouses along the border, where confusion stemming from President Trump's executive order is settling in.

Shane McMahon's client from El Salvador was charged with crossing into the U.S. illegally. He was separated from his 16-year-old son, and on Friday, those charges were suddenly dropped.

"I think what's happening is that everybody's trying to figure out how the order applies to us and what to do with it," McMahon said.

The Trump administration says that nearly 500 children have been reunited with family. More than 1,800 remain separated from parents, who are desperate for answers.

Handwritten notes saying "I do not know when i"ll be able to see my child again" are included in a lawsuit filed against the government by a jailed mother trying to find her child.

But Friday morning in Maryland, after nearly a month of separation, it was an emotional reunion for Beata Mejia-Mejia and her 7-year-old son, Darwin. They walked most of the way from Guatemala, crossing into the U.S. illegally when they saw American flags near the Arizona border.

Mejia-Mejia says they had no idea what a port of entry was or that they were breaking the law.

Editor's Note: This story has been updated to clarify that the children being reunited reflect only those in the custody of U.S. Customs and Border Protection.