There were many problems during the time of the Reformation. I will only name two of them. 

First, there was theological controversy. All you need to think about is Martin Luther and this ninety-five theses. In fact, the Protestant Reformation took place in large part because of theological differences. We should also keep in mind that Protestant theologians also disagreed with one another. 

Second, there was also problems of morality. A good example of this can be seen in John Tezel, who sold indulgences. A popular jiggle was: "As soon as a coin in the coffer rings, a soul from purgatory springs." This desire for money in some areas of the church was deeply problematic. 

In terms of what motivated the reformers, no simple answer can be given. Moreover, there were many reformers. However, we can say that there was some general similarities. The buzz phrase during the Reformation was "ad fontes," back to the sources. Therefore, there was a huge push to go back to the doctrine and practice of the early church.