The Pope hates El Opus, but the big problem is that an Argentinian was recently appointed as head of Opus Dei and they are not opposing this heterodox pope in any way, shape or form. And Opus Dei is not supporting its own members because it’s afraid of being suppressed or marginalized by Pope Francis.
Livieres was very good and nothing he did would have been in any way questionable...except that he was viewed as conservative (and despite the fact that his diocese yielded many, many more vocations than anywhere else in that region). He had enemies in his own country and in the more powerful Argentina, and Pope Francis obviously unleashed them.
The Jesuits hate Opus Dei, because they essentially replaced them as loyal supporters of the Pope. Having a Jesuit Pope complicates things still further.