Blessed John Paul II attempted early on in his pontificate to reform the Jesuit order with mixed results. Indeed, George Weigel claims that the Jesuits were like a thorn in the side of JPII--always evading his strategic reforms with more and more unorthodoxy:
(speaking of the election of Francis I)
I suspect there were not all that many champagne corks flying last night in those Jesuit residences throughout the world where the Catholic Revolution That Never Was is still regarded as the ecclesiastical holy grail. For the shrewder of the new pope’s Jesuit brothers know full well that that dream was just dealt another severe blow. And they perhaps fear that this pope, knowing the Society of Jesus and its contemporary confusions and corruptions as he does, just might take in hand the reform of the Jesuits that was one of the signal failures of the pontificate of John Paul II. GEORGE WEIGEL--http://www.nationalreview.com/articles/342964/first-american-pope-george-weigel?pg=3
Apparently, the Jesuits were more or less forerunners in the brain-child of liberation theology (please reference my 2012 post on "JPII vs Liberation Theology"). Not only that, but they espoused outlandish teaching on women's ordination, homosexual activity, and contraception. For an order that originally was formed to pledge absolute allegiance to the seat of St. Peter, Jesuits had fallen far away from the tree.
It is easy, then, to guess that JPII did very little to correct such disobedience. Likewise, it is easy to think him aloof in addressing problems that constantly arose during his days as Pope. On the contrary, JPII acted somewhat harshly on the Jesuits soon after their vicar general, Pedro Arrupe, passed away from stroke: