From http://carm.org/why-apocrypha-not-in-bible:
The Catholic Church has not always accepted the Apocrypha. The Apocrypha was not officially accepted by the Catholic Church at a universal council until 1546 at the Council of Trent. This is over a millennium and a half after the books were written, and was a counter reaction to the Protestant Reformation.
Many church Fathers rejected the Apocrypha as Scripture, and many just used them for devotional purposes. For example, Jerome, the great Biblical scholar and translator of the Latin Vulgate, rejected the Apocrypha as Scripture though, supposedly under pressure, he did make a hurried translation of it. In fact, most of the church fathers in the first four centuries of the Church rejected the Apocrypha as Scripture. Along with Jerome, names include Origen, Cyril of Jerusalem, and Athanasius.
The Apocryphal books were placed in Bibles before the Council of Trent and after, but were placed in a separate section because they were not of equal authority. The Apocrypha rightfully has some devotional purposes, but it is not inspired.
It is true that the Catholic Church accepted the Apocryphal books at earlier councils at Rome (A.D. 382), Hippo (A.D. 393), Carthage (A.D. 397), and Florence (A.D. 1442). However, these were not universal Church councils and the earlier councils were influenced heavily by Augustine, who was no Biblical expert, compared to the scholar Jerome, who rejected the Apocrypha as part of the Old Testament Canon. Furthermore, it is doubtful that these local church council's decisions were binding on the Church at large since they were local councils. Sometimes these local councils made errors and had to be corrected by a universal church council.
(Also, the earlier councils did not agree completely with each other either.)
The same could be said for James, 2,3 John, Hebrews, and Revelation, so what’s your point?
Some rejected Esther, so should you throw Esther out of your Bible because of that?
No Church council upheld the private opinions of these Church fathers the Qunisext Council definitively settled the issue of the scriptural canon as far as the Eastern Church was concerned.
Some early writers thought that sins couldn’t be forgiven after baptism either.
And these same fathers were hardly consistent with the disputed Old Testament books either, considering that many cited them as scripture when it suited them.
http://www.cin.org/users/jgallegos/deutero.htm
Will you start treating Revelation and Hebrews as apocryphal considering that many of these same writers thought they were apocryphal? I doubt it.
The Church overruled them on a universal level. Certain local theologians had their opinions on a local level, but it is a stretch to say that the “Catholic Church” ever defined against the disputed books. It takes a council to do that.