Why do some Bibles have extra-biblical books in them? Why were some books excluded from the Bible?
The Bible as we have it today, which consists of 66 books, took a very long, thoughtful process to come together. The church was able to discern which of the books were indeed inspired by God, and which did not belong in the Bible, so how did they know which ones belonged and which ones didn’t? Apparently, it was the early Church fathers who heavily influenced what books would be in the Bible and what books would be rejected. Trusted men of God like Polycarp, Justin Martyr, Tertullian, Origen, Eusebius, Athanasius, Jerome, Augustine, and others, all led the slow and careful acceptance of the books in the New Testament as we know it today. It was very early in the church’s history that the vast majority of books were accepted by the church as Scripture, mainly because the church leadership and membership had both accepted them as being from God. The New Testament books also fit the context of what was in the Old Testament, especially since many of the quotes from the New Testament authors were quotes taken directly from the Old Testament . This may explain why the early church, predominantly Jewish, was able to accept the New Testament books so easily.
Some alleged “lost books” of the Bible that had somehow been lost, have recently surfaced with the claim that these too are Scripture, and some even have other gospels that they believe should be in the Bible, but the vast majority of Bible scholars reject them, and for very good reason. One example is the Gospel of Judas, which completely contradicts the four gospels we have, like when Judas was said to have betrayed Christ because he was commanded to do so by the Lord, but other flagrant falsehoods in this book include Jesus supposedly marrying Mary Magdalene, and even claiming to have had children by her, but there is no biblical or historical evidence to support this, so it was an easy decision to reject the Gospel of Judas today. Other fake gospels or books of the Bible include, the Secrets of Enoch, the Conflict of Adam and Eve with Satan, Psalms of Solomon 4, the Gospel of Philip, the Apocalypse of Peter, and the Gospel of Mary, and you don’t have to be a Bible scholar to see that these books are not consistent with the 66 books of the Bible. They clearly don’t fit contextually and doctrinally with the Scriptures. Many other books such as 1 Maccabees, the Wisdom of Solomon, and other such books are what we call the Apocrypha, and these books have never been accepted as inspired by God, and all of these books were flatly rejected by the Jews. They have some interesting historical facts, but they also have glaring errors, and Jesus and the apostles never once quoted from these books, and the Jews rejected them as Scripture, and have to this day, refused to believe them as being part of the Old Testament. Maybe this is why the Apostle Paul said, “even if we or an angel from heaven should preach to you a gospel contrary to the one we preached to you, let him be accursed” (Gal 1:8), and these books preach another gospel; a gospel not from God.
Examples of False Scriptures
Today, and for thousands of years, the Apocrypha was not considered part of the holy canon, and for good reason. These books contain a large number of doctrinal errors, like in Tobit there is the command to use magic (Tobit 6:5-7), that forgiveness of sins comes from alms giving (Tobit 4:11; 12:9), and that we are to make offerings of money for the sins of the dead (2 Maccabees 12:43-45). All of these clearly contradict the biblical doctrine that our sins are forgiven only through Christ and His shed blood, and putting our trust in Him. Not only do these books contain serious doctrinal errors, they contain historical errors too. For example, the Book of Judith states that Nebuchadnezzar was the king of the Assyrians when he was actually the king of the Babylonians, and the Baruch states that the Jews would serve in Babylon for seven generations (Baruch 6:2), but Jeremiah 25;11 clearly states it will only be 70 years, so these are not just minor issues…they are serious doctrinal issues with dozens of historical errors, so they are not trustworthy at all, and should not be considered part of the inspired Word of God, which is perfect and without error. The 66 books of the Bible  are not a product of man, but the inspired Word of God (1 Tim 3:16).
Tested by Time
We can know that the 66 books in the Bible that we currently have are the inspired Word of God because the dozens of prophecies that were written hundreds, and sometimes, thousands of years before the events happened, and they took place exactly as prophesied. The Old Testament was widely accepted as inspired by God and has long since been considered to be the very Word of God. By the year AD 180, all of the New Testament books in the Bible, (with the only single exception, being 2 Peter) were directly quoted by church leaders, so the early church was clear on what was considered Scripture and what was not, and even though some churches hesitated over the books of James, Jude, 2 and 3 John, 2 Peter, Hebrews, and Revelation, all other books in the Bible were universally accepted by the church, and it wouldn’t be long before all 27 books of the New Testament would be accepted as God’s Word. It’s also important to note that the early church leaders never once used non-canonical or apocrypha books in their writings or teachings, and they never treated these other books with the same kind of reverence and authority that they did the New Testament books. The early church was not that far removed from studying the teachings of Jesus, which at that time called, “the apostle’s doctrine” (Acts 2:42), so even in the first century church, they stressed the teachings of Jesus, and they were of such supreme importance, that the gospel authors were inspired by God to record Jesus’ earthly ministry.
I believe we can trust the Bible that we have today…the Bible which contains 66 books, written by approximately 40 authors, because it has been shown to be the living, active Word of God that can even penetrate our thoughts, intentions, and motives of the heart (Heb 4:13). The many fulfilled prophecies, the thousands of archaeological discoveries, and the endurable Word of God provides more than enough for us to know that when we pick up the Bible, it is God speaking to us; it is His inspired Word; and it is all that we need to know how to be saved. With anything other than these 66 books, you’re taking chances…chances I’m not willing to take. I want the truth. How about you?
Related reading for you here: What Are the Apocrypha Books? 
Resource – Scripture quotations are from The Holy Bible, English Standard Version® (ESV®), Crossway Bibles. (2007). ESV: Study Bible : English standard version. Wheaton, Ill: Crossway Bibles. Used by permission. All rights reserved.