While Mary MacKillop might have been a saint after her death, she had her share of conflicts when alive. In 1871, she was excommunicated because of insubordination. However, the decision was reversed a year after. Conflict continued among bishops as to control the nuns, whether it was the local Bishop or the superior of the other. She travelled to Rome and obtained a qualified approval that allowed her to set up a central government. The Bishop of Bathurst was not happy with this and requested control in his diocese, which led to a split.
The decision of the Vatican also enforced more lenient poverty than what MacKillop wished for, and this was considered to be a battery of the vision by Julian Tenison Woods, the co-founder of the order, causing a disagreement that was never ultimately settled.
The Bishop of Adelaide also asked MacKillop to leave in 1883, which she refused. Thus, Cardinal Moran informed her in 1885 that her reflection to be a superior general was invalid.