According to When Skeptics Ask (Normal L. Geisler and Ronald M. Brooks, 1990 Baker Books):
The following books were in question at one point or another:
- Hebrews because the author is unknown. However, it was accepted as having apostolic authority, if not apostolic authorship.
- James because of conflict with Pauls teaching about salvation by faith alone. Conflict resolved by seeing works as an outgrowth of faith.
- 2 Peter because the style differs from 1 Peter. But Peter used a scribe to write 1 Peter (See 5:12), who may have helped him smooth out his Greek.
- 2 and 3 John because the author is called "elder" not apostle. However, Peter called himself an elder, too (1 Peter 5:1). They are also cited in earlier lists of canon.
- Jude because he refers to the book of Enoch and the Assumption of Moses. However, he doesn't call them Scripture, and this is seen to be like Paul quoting pagan poets (such as in Acts 17:28 and Titus 1:12). It also had wide early acceptance.
- Revelation because it teaches a thousand year reign of Christ, which was taught by a certain cult. However, it was accepted by the earliest Church fathers.
This is somewhat of a side note, but it is worth noting that the thought that some of the books now considered canon were ever disputed might cause some confusion over whether the right books are in Scripture. That is a common question both from the faithful and from skeptics.
My intention here is not to raise the question again. In order to head those questions and comments off, I'll just point out that it's been answered time and time again, as it is here: http://www.worldviewweekend.com/worldview-times/article.php?articleid=1701
The question which invariably arises when speaking of the Scriptures
is, "How does one know which books in today's Bible are the right
ones?" It is important to note at this point that a group of men did
not just arbitrarily select a group of books to be used in compiling
the Bible. They only officially "recognized" which books had always
been upheld as being scriptural.
some details removed. Check the link if you care to see what's missing. Conclusion from the article below:
A crisis in the fourth century caused the Church to give a formal
statement on which books were canonical. In A.D. 397, a Church Council
was held in Carthage which endorsed the exact 27 books of the New
Testament we now regard as canonical. These 27 books were all
apostolic in origin, authoritative in spiritual content, and accepted
universally among the orthodox churches. These tests were used at the
council to eliminate the spurious gospels and epistles written by
heretical groups. This process of canonization has ensured that
today's Bible contains only the books which were attested as being
inspired by God.