Steve Ray has a list of 35 loaded Questions for "Bible Christians" (quotation marks his)(link to the whole list). This is number 15/35. I'm trying to provide the answers in a common format, for easy reference.
15) If the books of the New Testament are “self-authenticating” through the ministry of the Holy Spirit to each individual, then why was there confusion in the early Church over which books were inspired, with some books being rejected by the majority?
There was disagreement (confusion is not the right term) for a variety of reasons. One of the reasons for the disagreement arose because of human traditions: if a book was not included in the calendar of liturgical readings, this sometimes lead folks to question whether it was Scripture; or, if the book made it into a collection of Greek writings alleged to be the Old Testament Scriptures, it was taken for granted that this had been part of the Jewish Scriptures.
1) The fact that the Holy Spirit authenticates his Word to believers doesn't guarantee each believer that he will be 100% right about every last book or about every last part of every last book, or about ever last word, jot and title of every passage.
2) There doesn't appear to ever have been any significant uncertainty about most of the New Testament books like the gospels or Paul's epistles - especially the gospels.
3) There likewise doesn't appear to have been any significant uncertainty about more than one or two of the 37 canonical Old Testament books.
4) What should be truly remarkable for Mr. Ray is the fact of Protestantism's virtually unanimous acceptance of the 66 book canon (there are a few that would get lumped in with "Protestants" that would try to eliminate one or more books, but they are an insignificantly tiny minority).