Humane Treatment of Migrant Children Act This bill prohibits an agent or officer of the Department of Homeland Security (DHS), the Department of Justice (DOJ), or the Department of Health and Human Services from removing a child (i.e., an individual who has not reached the age of 18 and has no permanent immigration status) from a parent or legal guardian at or near the port of entry or within 100 miles of the U.S. border unless: (1) a state court determines that such removal is in the best interests of the child, (2) a state child welfare agency makes a similar determination because the child is in danger or abuse or neglect, or (3) the Chief Patrol Agent or the Area Port Director authorizes separation based on a finding that the child is a victim of trafficking or is in danger of abuse or neglect. The bill establishes a strong presumption in favor of family unity and a presumption that detention is not in the best interest of families and children. It further requires DHS to ensure that sibling groups remain intact. DHS must: (1) publish final public guidance that describes the manner in which a parent or legal guardian may locate a child who has become separated; (2) provide the parent or legal guardian of a separated child basic information about the child's activities, education and health, and immigration status; and (3) report to Congress annually on family separation. The Government Accountability Office must study, and report on, the prosecution of asylum seekers during the period beginning on January 1, 2008, and ending on December 31, 2018. The bill requires that unaccompanied alien children be provided free legal counsel in immigration proceedings and that DHS provide access to counsel for all aliens detained in immigration detention facilities. The U.S. Immigration and Customs Enforcement shall use its resources to detain aliens who pose a threat to national security or public safety. Aliens shall not be detained if they are known to be suffering from serious physical or mental illness, have a disability, are elderly, pregnant, or nursing, are minors, are the primary caretakers of a minor or an inform person, or that their detention is otherwise not in the public interest. DHS must provide sufficient funding to cover alternatives to detention programs. DOJ must increase the total number of immigration judges and DHS must increase the number of its personnel responsible for processing refugee applications.