The reason for this, I believe, is that Rome certainly did not have its act together at the time of the Reformation. An image that comes to mind is one of Keystone Cops running around trying to decide what to do about Luther [given that they did not have an easy way to kill him].
Here, from the Reformation historian Patrick Collinson, is an example of how Rome dealt with “uncomfortable” information in that era:
In 1543 a little book was published in Venice with the title Trattato utilissimo del beneficio di Giesu Christo crocifisso i cristiani (A Most Useful Treatise on the Merits of Jesus Christ Crucified for Christians), written by an elusive Benedictine monk called Benedetto da Mantova (dates of birth and death unknown, but his surname seems to have been fontanino) with some help from the humanist and poet Marcantonio Flaminio (1498-1550), a popular work of piety that was translated into several languages including Croat. At first sight this may appear to be a piece of native Italian Christocentrism, part of a Pauline and Augustinian renaissance known to have been nourished by a Spanish humanist and biblicist, Juan de Valdes (1500-1541), whose pious circle in Naples had included Flaminio. But the Beneficio can be read in more than one way. It proves to have been made up from a number of transalpine Protestant texts, and especially the 1539 edition of Calvin's Institutes. Whether or not Benedetto had come across Calvin in his monastery on the slopes of Mount Etna, which seems unlikely, the Institutes was known to Flaminio.I don’t think it’s too much of a stretch to say that “official Rome” was embarrassed by many of the things its own apologists were saying, and it certainly had the ability to deal with embarrassing information.
It is hard to distinguish between the theology of the Beneficio and Protestantism. "Man can never do good works unless he first know himself to be justified by faith." Other scholars insist, however, that the Beneficio is an expression of Evangelism, a movement that was not generated by Protestantism and should be distingueshed from it. What is certain is that the Beneficio was placed on the Index and so successfuly repressed by the Roman Inquisition that of the many thousands of copies of the Italian edition that were once in existence only one is known to survive, discovered in the library of a Cambridge college in the nineteenth century. That sort of successful repression was the Counter-Reformation. (The Reformation, a History, Patrick Collinson, (c)2003, pgs 105-106.)