Are there books that are included in the Protestant Bible that were disputed as canonical?

Question

The topic of how the Bible was compiled, including the determining factors for which books are included is well-documented. There were some basic criteria as listed at http://gracethrufaith.com/ask-a-bible-teacher/how-was-the-bible-compiled/

1. Were the authors either eyewitnesses to the events they wrote about or at least directly taught about them by the Apostles?
2. Was each book’s teachings consistent with church practice and tradition?
3. Was each book already in general use by the church, and accepted as the Divine Word of God?

We've also had several questions on the site about why [Name an apocryphal book] was not included in Scripture. However, I've never seen the question asked:

Are there books that are included in Canon that were once disputed or questioned, that remain in the Bible. If so, why were they disputed, and why did they "pass the test"?

Answer 1

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.

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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

Excerpt:

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.

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some details removed. Check the link if you care to see what's missing. Conclusion from the article below:

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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.