A fair criticism, but let's not forget these facilities and practices were opened during the Obama administration. People like to point to this as a point of criticism against Trump.
Can't read the article because it's behind a paywall, but unfortunately I've come to doubt anything the NYT reports against Trump as they tend to be less than honest about how they choose to report and represent things.
And my understanding is that those facilities and practices were put into place to protect the children from assault by the predominantly adult population of the then-existing detainment facilities.