Sadly, our Christian friends are discovering, due to the dishonesty of the Gospel writers/Bible scribes, they have been misled – that’s to say they are realising they have been conned. However, Christian forgery (deception) has been so rampant that it appears that zealous Trinitarian Christians even tampered with the work of the Jewish historian Josephus in order to work their Trinitarian Christian agendas.
Before discussing the possible deceptive Christian alterations of Josephus’ work let’s discuss another problematic account within the Gospels – Matthew 2:16:
When Herod realized that he had been outwitted by the Magi, he was furious, and he gave orders to kill all the boys in Bethlehem and its vicinity who were two years old and under, in accordance with the time he had learned from the Magi. [NIV, Matthew 2:16]
Matthew 2:16 depicts Herod as murdering all the young male children in Bethlehem. You would expect this act to have been chronicled by Josephus.
Yet, significantly, the massacre of Bethlehem’s young boys which is mentioned in Matthew finds no place even in the bloody history of Herod that Josephus recorded! Certainly such an event had it really happened, would have been mentioned in a historical record that narrates, amongst other details of the history of Herod, his brutal actions. Again, the conclusion must be that the massacre that Matthew details has no place in history. It should be stressed here, however, that this is not a form of negative evidence, for Josephus did record a detailed history of Herod in which the alleged massacre does not figure at all. 
Josephus chose not to record it?
Our Christian apologist friends may claim Josephus deliberately chose not to record “the massacre” as Josephus disagreed with the theological conclusion of Herod. However, this style of argumentation is inconsistent as Josephus alleged accounts of Jesus are indeed supportive of Christian theology.
The account in the Jewish War calls Isa [Jesus] a “miracle-worker”, attributing to him various miraculous acts, and goes as far as suggesting that “man” might not be the right word to describe him (Josephus, JW:398-400)!
Josephus also wrote Isa [Jesus] was raised from the dead the third day after his crucifixion. All these claims are mentioned more briefly in another of Josephus’ books, Jewish Antiquities, in which the Jewish writer goes that step further and claims that Isa was al-Masih [Messiah] (Josephus, JA, XVII: 63-64)! 
What didn’t the Christians forge?
It appears early Trinitarian Christians were not only busying themselves in adding forgeries to the Bible but were also tampering with the work of Josephus:
Critics have thrown doubts on the authenticity of Josephus’ supposed accounts of Isa [Jesus] which sounded too Christian to have been written by the Jewish historian. Other scholars, on the other hand, accept the genuineness of those accounts arguing that they contain points that cannot be reconciled with Christian tradition and they do not reflect a writer with a Christian faith but rather depict him as a doubting onlooker (Williamson, 1974: 396-397).
However, critics have raised a number of strong points against the authenticity of the controversial passages. Concerning the account in the Jewish War, the main argument of critics is that the piece about Isa [Jesus] is found in the Slavonic version of Josephus’ book but not in the Greek version. The principle arguments against the genuineness of the account in the Jewish Antiqiuities are as follows:
(i) The Jewish Josephus could not have described Isa [Jesus] as al-Masih [Messiah]
(ii) While the bishop and historian Eusebius of Caesarea (d. ca. 340 CE) mentions the controversial passage, the Greek theologian Origen (ca. 185-254 CE) had expressly stated that Josephus did not believe Isa [Jesus] to be al-Masih; and finally
(iii) The suspicious passage breaks continuity of Josephus’ description of a series of riots (Feldman, 1965:49)
Most scholars do not accept the authenticity of the two accounts in Josephus about Isa [Jesus]. In all probability, these references to Isa [Jesus] are inauthentic and must have been forged by Christians, but this is not relevant to our present discussion. 
Tough question for our Christian friends…
Whether the passages about Isa in Josephus’ works are genuine or not they still raise the following significant question: Why would the writer of those two accounts fail to make any reference to the alleged killing of the young boys that was intended to kill boy Isa? The answer cannot be anything other than that writer had no knowledge of the alleged massacre.
 History Testifies to the Infallibility of the Quran – early History of the Children of Israel – Dr Louay Fatoohi and Prof. Shetha Al-Dargazeli, Adam Publishers and Distributers, 1999, p 203-205