Because she sued for wrongful termination on the basis of gender discrimination (and retaliation), she apparently alleged that whatever insubordination reason the Church claimed to fire her, it was really based on the fact that she was a woman.  

So, the most obvious example of that would be that she became pregnant out of wedlock, and the Church fired her.  Another example could be that she was fired for overtly complaining (perhaps to her students) that she wanted to be a priest but the Church wouldn't let her, but I can't imagine a lawyer taking such a case as a gender-discrimination claim, because a man could have made the same complaint about the Church's teaching on women priests.  Maybe she was dressing with her cleavage showing, but that's a very weak gender claim too.

If she were married and the Church fired her for being pregnant, then the ministerial exception clause is unfairly depriving her of a legitimate claim, and the Court is wrong, imo.  All speculation w/o facts.