Investigations found evidence that several districts refused to enroll undocumented youths and unaccompanied minors if they were unable to produce documents demonstrating guardianship or residency in the state.
The White House saw the programs, which could shield as many as 5 million undocumented immigrants from deportation, as tools to ease concerns about separating school-aged children from their families.
Interior Secretary Sally Jewell acknowledges that "we're at a time in our nation's history where we have awakened to the fact that we are not doing an effective job serving Native youth."
The students, many of them undocumented immigrants from Central America, have to juggle court dates and concerns about deportation while trying to adjust to schools in a new country.
In its first report, the group's founder argues that "DLLs have long been ignored in education policy debates."
The longtime educator says English-learners are a population of students who are "historically underserved," but she expects that to change.
Two disability advocacy organizations filed a Justice Department complaint on the parents' behalf, saying that seven Ohio districts were failing to translate documents or provide interpreters.
The president's proposed fiscal year 2016 budget would raise spending levels for those programs to $773 million, an increase of nearly 5 percent.
The request, which is $150 million more than the current federal budget, would allocate nearly $60 million in new funding for repairing schools and new construction.
Classification policies and evaluation tools can vary widely from state to state, and even district to district, leaving widespread opportunity for error.