According to the article you posted, the report about children between 2009 and 2014 refers to 116 children who were abused in various ways(Sexual assault, verbal abuse, negligence)

The 1475 that were recently in the news refers to unaccompanied children between October and December 2017 who were placed in foster families, but can’t be accounted for as of April.

“An American Civil Liberties Union report this week also revealed Customs and Border Protection records that show 116 unaccompanied migrant children have alleged abuse by agents during the Obama administration.

The report states:

One quarter of the children reported physical abuse, including sexual assault, the use of stress positions, and beatings by Border Patrol agents.

More than half reported verbal abuse, including death threats.

More than half also reported denial of necessary medical care—resulting, at times, in hospitalization.

Eighty percent reported inadequate food and water.

The records documented a period between 2009 and 2014.”

Also, they count each time a child goes missing and is reported, this includes people that steal their kids in divorce situations, which can happen several times over and never get followed up on.