There was no indisputable (“infallible”) definition of the entire Catholic canon of Scripture for most of Catholic history, and until after the death of Martin Luther in 1546, and who, along with other scholars, was at liberty to doubt or disagree on the contents of the canon.
The apocryphal books, referred to in Catholicism as the Deuterocanonical books (Deuteros for short) were subjects of scholarly doubts and disagreements down thru the centuries and right into Trent, which provided the first “infallible”) definition of the entire Catholic canon of Scripture for Catholics. Catholisc such as Origen, Athanasius, Cyril of Jerusalem, Gregory of Nazianzus, Rufinus , Jerome etc., relegated the deuteros to inferior rank, not being Scripture proper, and thus fit for "confirmation of the doctrine of the Church"(Jerome), but yet edifying literature, which could be sometimes cited as scripture.
Cyril of Jerusalem (d. circa. 385 AD) even exhorted his readers “Of these read the two and twenty books, but have nothing to do with the apocryphal writings. Study earnestly these only which we read openly in the Church. Far wiser and more pious than thyself were the Apostles, and the bishops of old time, the presidents of the Church who handed down these books. Being therefore a child of the Church, trench thou not upon its statutes. And of the Old Testament, as we have said, study the two and twenty books, which, if thou art desirous of learning, strive to remember by name, as I recite them.” (Cyril of Jerusalem on the Canon)
The Catholic Encyclopedia states as regards the Middle Ages, In the Latin Church, all through the Middle Ages [5th century to the 15th century] we find evidence of hesitation about the character of the deuterocanonicals. There is a current friendly to them, another one distinctly unfavourable to their authority and sacredness, while wavering between the two are a number of writers whose veneration for these books is tempered by some perplexity as to their exact standing, and among those we note St. Thomas Aquinas. Few are found to unequivocally acknowledge their canonicity. The prevailing attitude of Western medieval authors is substantially that of the Greek Fathers. The chief cause of this phenomenon in the West is to be sought in the influence, direct and indirect, of St. Jerome's depreciating Prologus (Canon of the Old Testament) ^
3. With the above as support, Luther included (most of) the deuteros in his translation of the Bible, but together as a separate section, as per an ancient practice. And sometimes quoted from within it.
4. The Eastern Orthodox churches do not fully agree with the canon of Trent.
5. The Palestinian canon of the time of Christ is though to have been restricted to 22 books, which correspond (due to 2 books being counted as one) to the 39 book Protestant canon, and that its tripartite division Christ referred to in Luke 24:44.
6. For many reasons it is held that the Septuagint is of dubious support for the apocrypha. There is no extant copy of the Septuagint from time of Christ, and the evidence indicates it did not contain the deuteros.
7. The idea of the Jewish canon being set at a council of Jamnia is dubious.
8. The Dead Sea Scrolls “included not only the community's Bible (the Old Testament) but their library, with fragments of hundreds of books. Among these were some Old Testament Apocryphal books. The fact that no commentaries were found for an Apocryphal book, and only canonical books were found in the special parchment and script indicates that the Apocryphal books were not viewed as canonical by the Qumran community. — The Apocrypha - Part Two Dr. Norman Geisler http://www.jashow.org/Articles/_...
9. Long before a church presumed it was essential for ascertaining what (men and writings) was of God, common God-fearing Jews rightly did so, and thus the church began with such doing so.
10. The establishment of inspired writings of God as being so is not due to conciliar decrees, as helpful as they can be, but is essentially due to the Divine qualities and attestation of such by people free to choose.
11. Luther (who also doubted Revelation, for one) did not set the canon for Protestants.
12. The OT Protestants canon is more ancient than that of Catholicism, canon, as even the Catholic Encyclopedia affirms, “the protocanonical books of the Old Testament correspond with those of the Bible of the Hebrews, and the Old Testament as received by Protestants.” “...the Hebrew Bible, which became the Old Testament of Protestantism.” (The Catholic Encyclopedia>Canon of the Old Testament.
13. In contrast to the Catholic claim of extraScriptural wholly inspired revelation preserved in oral tradition, and which is made equal to that which is written (as decreed by non-inspired men, who are effectively the supreme authority), writing is God's manifest means of long term reliable authoritative preservation. (Exodus 17:14; Exodus 34:27; Deuteronomy 10:4; Deuteronomy 17:18; Deuteronomy 27:3; Deuteronomy 31:24; 2 Kings 22:10-13; Isaiah 30:8; cf. Job 19:23; John 20:31; Revelation 20:12, etc.)
14. Unlike writings in the Protestant OT canon, the NT never quotes from Deuterocanonical books as being "Scripture," or terms such as "it is written," "Moses said" which denote inspired authority. It is thought that the NT references to Scripture are affirming a Palestinian canon, which tripartite canon the Lord is seen referring to in Luke 24:44,45, which He calls Scriptures.
15. The word of God/the Lord was normally written, even if sometimes first being spoken, and that as written, Scripture became the transcendent supreme substantive standard for obedience and testing and establishing truth claims as the wholly Divinely inspired and assured, Word of God. As is abundantly evidenced.