The great power and wealth of the Church led to many abuses. There was a certain cyclic character to these. A particularly strong Pope or a reforming Church council would stamp out some of the abuses, and things would be okay for a while, but sooner or later they would spring up again.
These abuses took many forms. For example;
Worldliness: High living, and loose living, by memebrs of the clergy. High ranking churchmen tended to have to live like nobles, in order to compete with them in terms of power and influence. But there were limits, and often even parish priests, monks, and nuns lived quite luxurious lives, in violation of their vows. The church preached the simple life, particularly for the clergy. But human nature being what it is...
Sins of the Flesh: Violations of vows of celibacy , a failure by no means limited to male member sof the clergy, for one occasional hears of convents dissolved for "excessive immorallity.".
Lay Investiture: The granting of Church positions to persons who were not members of the clergy, as, for example, when a king might try to get a bishopric for his favorite courtier.
Nepotism: High churchmen using their influence to secure posts for the kinfolk. including their "nephews."
Simony: The offering of bribes to secure positions, such as a rich parish, by a member of the clergy.