Always has been. Julie of the Wolves is a Newbery winner and the sexual assault in the first quarter of the book is central to the entire story. The Giver is another, and deals with euthanasia and infanticide (literally 'abortion after birth'). Number the Stars, again a Newbery winner, dealing with escaping genocide. The Slave Dancer - guess that topic? Summer of the Swans, with a mentally disabled sibling? Shiloh - animal abuse. Maniac Magee - racism.
And they've always been being banned for these things. And these are just from the <100 Newbery winners.