The serious problems in the Church were largely caused by the decline of the Church’s temporal power and the rising power of secular monarchies in Europe.
At the end of the 13th century, the Church started to come into conflict with secular monarchies. Monarchs like King Philip IV of France started to try to assert power over the Church. Philip, for example, claimed the right to tax French clerics and the right to put clergy on trial for certain crimes. In short, the real issue was whether secular rulers would be sovereign or the papacy would hold control because of its control over religious matters.
As part of this conflict, Philip actually had the Pope arrested. He then pressured the College of Cardinals to appoint a French Pope who took up residency in Avignon. This led to a drop in papal prestige as people came to think that the Pope was nothing more than a pawn of the French monarchy.
Once the Avignon papacy ended, the Great Schism began. Now, there were two popes. One was backed by the French and another by the Romans. All of the rest of Europe then had to take sides in the conflict. Of course, with two rival popes claiming power and with political fighting over which pope would be the “real” pope, the Church could not help but lose prestige. People came to view the Pope and the Church with much less respect than they previously had.
In short, the serious problems faced by the Church came about largely because of the Church’s attempt to maintain temporal power at a time when secular monarchies were becoming stronger and were attempting to use the Church to further their own ends.