At the Council of Nicaea, according to Protestant apologist Norman Geisler (How we Got the Bible, with co-author William E. Nix, Chicago: Moody Press, 1974, 109), the books of James, 2 Peter, 2 and 3 John, and Jude, were "named as disputed." Geisler seems, however (based on his comments on p. 111), to merely be talking about the time period of 325-340, and to base his conclusion on Eusebius' summary in Ecclesiastical History (III, 25, 3)...
In any event, there is considerable evidence that all these books were disputed by not a few until late into the 4th century: some of which I have discussed in other installments of this four-part reply.
Catholics often cite such disputes as if they're problematic for the Evangelical. But what does Dave think the disputes prove? They seem to have involved a minority's rejection of the books rather than a majority rejection. What does Dave think he's proving, then?
He goes on:
The Codex Sinaiticus manuscript from the late fourth century included the Epistle of Barnabas and the Shepherd of Hermas. The Codex Alexandrinus in the early fifth century included 1 and 2 Clement.
Again, what does Dave think he's proving? Manuscripts and Bibles often include documents that their producers or readers didn't consider scripture. Documents would often be reused or placed together in order to conserve resources, for example, or documents of a non-scriptural religious nature would sometimes be combined with documents viewed as scripture.
We often do such things today. Bibles will include passages or books that only some readers consider scripture, such as Apocryphal books in the Old Testament. Eldon Epp refers to some ancient manuscripts that contain New Testament books or portions of New Testament books, but also portions of documents obviously not considered scripture, such as "a history of Rome by Livy" and "a Christian letter" (in Lee McDonald and James Sanders, edd., The Canon Debate [Peabody, Massachusetts: Hendrickson Publishers, 2002], n. 16 on p. 490). Epp also notes that Codex Alexandrinus originally included eighteen Psalms Of Solomon (p. 493). He refers to a codex containing the Nativity Of Mary and 3 Corinthians, for example (p. 492). Does Dave want to argue that there was significant ancient support for the canonicity of works like Second Clement, the Psalms Of Solomon, and the Nativity Of Mary?
It's true that a book like The Shepherd Of Hermas will sometimes be referred to as scripture by the patristic sources. Its canonicity seems to have been accepted by only a small minority of Christians, however. See here. As I note in that article, Tertullian refers to The Shepherd Of Hermas as generally rejected by Christians, and he contrasts that rejection with the wider acceptance of Hebrews (On Modesty, 10, 20). Even though Hebrews is often categorized as one of the disputed books of the New Testament, it seems to have been much more widely accepted than documents like The Shepherd Of Hermas.
This is a strange place for Jason to try to make some sort of case for proto-Protestantism in the fathers, for the canonical disputes of those times are exceedingly complicated. The disputes are at the "edges" of the canon (mostly about books other than the Gospels and Paul's epistles).
In the same fashion, the disputes about the papacy and Roman primacy and the authority of same are about the "edges" and particulars: but not about the thing itself.
Keep in mind what I said earlier about the history of the papacy. The concept is absent and widely contradicted early on. When it first appears in the historical record around the middle of the third century, it's denounced by bishops in the West and East. Read what Firmilian wrote in response to Stephen. Do Firmilian's comments come across as part of a "dispute around the edges", but not about the papacy itself? When a Catholic historian like Joseph Kelly refers to the rejection of the Roman bishop's universal jurisdiction by the Eastern bishops at the Council of Nicaea (a council at which the large majority of bishops were Eastern), for example, does such a view of the bishop of Rome seem like a "dispute around the edges"? Is universal jurisdiction just a minor aspect of the papacy? If so, should we conclude that Eastern Orthodox accept the papacy, since they can affirm some type of "Roman primacy" without accepting the universal jurisdiction of the bishop of Rome?
As I've argued elsewhere, it seems that even the most disputed books of the New Testament were accepted by a majority during the ante-Nicene era. I'm not aware of any reason to conclude that any of the twenty-seven books had been rejected by a majority.
And it would be reasonable for a document like James or 3 John to not be mentioned often in the earliest generations of church history, given the brevity of the documents, the narrow scope of their relevance to what the early sources were discussing, and other factors involved. In contrast, the early absence of any reference to a papacy makes far less sense, if there was widespread belief in a papacy at the time. I explained some of the reasons why in an earlier response to Dave. If Irenaeus doesn't cite 3 John when arguing against the Gnostics, then his failure to cite that document doesn't have much significance for its canonicity. Why would we expect him to cite 3 John? But if he says nothing about a papacy when writing at length on issues of authority, even when discussing Roman primacy specifically, then that's a more significant problem for Roman Catholicism.