1. In Genesis 5:4, Adam and Eve don't have daughters until after the birth of Seth. However, in both Josephus and the Josephs Smith Translation of the Bible (JST), Adam and Eve have daughters at the same time Cain and Able are born.
Adam and Eve had two sons...they had also daughters. (Antiquities of the Jews 1:2:1)
And Adam knew his wife, and she bare unto him sons and daughters...and from that time forth, the sons and daughters of Adam began to divide, two and two, in the land. (Gen. 4:2-3 Joseph Smith Translation)
2. Although there's no mention of it in the Bible, both Josephus and Joseph Smith tell us that Cain became the leader of a wicked organization.
But Cain was not only very wicked in other respects, but was wholly intent upon getting...He augmented his household substance with much wealth, by rapine and violence; he excited his acquaintance to procure pleasures and spoils by robbery, and became a great leader of men in wicked courses. (Antiquities of the Jews 1:2:1-2)
And Cain said: Truly I am Mahan, the master of this great secret, that I may murder and get gain. Wherefore Cain was called Master Mahan, and he gloried in his wickedness. And Cain went into the field, and Cain talked with Abel, his brother. And it came to pass that while they were in the field, Cain rose up against Abel, his brother, and slew him. (Genesis 5:16 Joseph Smith Translation, also Moses 5:31-32)
As an aside, this passage of Mormon scripture is quoted in the video game Assassin's Creed II. A later passage in the Mormon scripture called The Book of Moses makes it clear that this was the founding of a secret Satanic society:
For Lamech having entered into a covenant with Satan, after the manner of Cain, wherein he became Master Mahan, Master of that great secret which was administered unto Cain by Satan; and Irad, the son of Enoch having known their secret, began to reveal it unto the sons of Adam. Wherefore Lamech, being angry, slew him, not like unto Cain, his brother Abel, for the sake of getting gain, but slew him for the oath’s sake. For, from the days of Cain, there was a secret combination, and their works were in the dark, and they knew every man his brother. (Moses 5:49-51)
3. The Bible makes no mention of Noah's life being in danger, but both Josephus and Joseph do.
For the tradition is that these men did what resembled the acts of those whom the Grecians call giants. But Noah was very uneasy at what they did; and being displeased at their conduct, persuaded them to change their dispositions and their acts for the better: and seeing they did not yield to him, but were slaves to their wicked pleasures, he was afraid they would kill him, together with his wife and children. (Antiquities of the Jews 1:3:1)
And in those days there were giants in the earth, and they sought Noah to take away his life...For it repenteth Noah that I have created them; and he hath called upon me, for they have sought his life. (Genesis 8:6,15 Joseph Smith Translation)
4. The Bible doesn't tell us that Abraham had astronomical knowledge, but again, both Josephus and Joseph do.
In the tenth generation after the Flood there was among the Chaldeans a man [Abraham] righteous and great, and skillful in Celestial Science. (Antiquities of the Jews 1:7:2)
And it is given unto thee [Abraham] to know the set time of all the stars that are set to give light, until thou come near unto the throne of God. (Abraham 3:10)
Also, Fascimile 3 in the Pearl of Great Price depicts Abraham instructing the king of Egypt in the "principles of astronomy".
5. In Genesis, Jacob gives a blessing to his son Joseph upon his deathbed dealing with his descendants. He does not praise Joseph himself in the Bible, but he does in Josephus' version:
Now when Jacob had lived seventeen years in Egypt, he fell into a disease, and died in the presence of his sons; but not till he made his prayers for their enjoying prosperity, and till he had foretold to them prophetically how every one of them was to dwell in the land of Canaan. But this happened many years afterward. He also enlarged upon the praises of Joseph, how he had not remembered the evil doings of his brethren to their disadvantage. (Antiquities of the Jews 2:8:1)
The Joseph Smith Translation also has Jacob praise Joseph:
And Jacob said unto Joseph when the God of my fathers appeared unto me in Luz, in the land of Canaan; he sware unto me, that he would give unto me, and unto my seed, the land for an everlasting possession. Therefore, O my son, he hath blessed me in raising thee up to be a servant unto me, in saving my house from death; In delivering my people, thy brethren, from famine which was sore in the land; wherefore the God of thy fathers shall bless thee, and the fruit of thy loins, that they shall be blessed above thy brethren, and above thy father’s house; For thou hast prevailed, and thy father’s house hath bowed down unto thee, even as it was shown unto thee, before thou wast sold into Egypt by the hands of thy brethren; wherefore thy brethren shall bow down unto thee from generation to generation, unto the fruit of thy loins forever; For thou shalt be a light unto my people, to deliver them in the days of their captivity, from bondage; and to bring salvation unto them, when they are altogether bowed down in sin. (Joseph Smith Translation of Genesis 48:5-11)
6. According to the Bible, Moses died a natural death. According to Josephus, he did not die, but was taken up to God.
As he was going to embrace Eleazar and Joshua, and was still discoursing with them, a cloud stood over him on the sudden, and he disappeared in a certain valley, although he wrote in the holy books that he died, which was done out of fear, lest they should venture to say that, because of his extraordinary virtue, he went to God. (Antiquities 4:8:48)
The Joseph Smith Translation of Deuteronmy 34 leaves the account of Moses's death as is, however, the Book of Alma tells us Moses was taken up to God.
And when Alma had done this he departed out of the land of Zarahemla, as if to go into the land of Melek. And it came to pass that he was never heard of more; as to his death and burial we know not of. Behold this we know, that he was a righteous man; and the saying went abroad in the church that he was taken up by the Spirit, or buried by the hand of the Lord, even as Moses. But behold, the scriptures saith the Lord took Moses unto himself, therefore, for this cause we know nothing concerning his death and burial. (Alma 45:18-19)
7. In the Bible, Abraham's wife Sarai was his half-sister. In the writings of Josephus and Joseph Smith, Sarai is his niece.
Now Abraham had two brethren, Nahor and Haran; of these Haran left a son, Lot; as also Sarai and Milcha his daughters, and died among the Chaldeans, in a city of the Chaldeans, called Ur; and his monument is shown to this day. These married their nieces. Nahor married Milcha, and Abram married Sarai. (Antiquities 1:6:5)
And it came to pass that I, Abraham, took Sarai to wife, and Nahor, my brother, took Milcah to wife, who were the daughters of Haran. (Abraham 2:2, note: this scipture was changed in 1981 so current Mormon scripture does not have Abraham marry his niece.)
D. Michael Quinn tells us in Early Mormonism and the Magic World View that the Palmyra bookstore and library had copies of Josephus during Joseph Smith's time. We also know Joseph Smith read Josephus while he was in jail the night he was murdered. It's likely that Joseph Smith was influenced by the writings of Josephus, however many of the places where he diverges from the Bible could have come from other sources as well.
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