So the first thing you notice with the Gospel of John is that there are theological differences between it and the Synoptic gospels. The authors of Matthew and Mark claim that John the Baptist is the Elijah while the author of the 4th gospel has John the Baptist himself openly speaking words denying those claims. Malachi 4:5-6 is the prophecy concerning the return of Elijah as the forerunner to the Messiah.

“For all the Prophets and the Law prophesied until John. And if you are willing to receive it, he is Elijah who is to come.” (Matthew 11:13-14, also see Mark 9:12-13)

“Now this is the testimony of John, when the Jews sent priests and Levites from Jerusalem to ask him, “Who are you”…And they asked him, “What then? Are you Elijah?” He said, “I am not.”” (John 1:19-21)

Jesus’ ministry in the Synoptic gospels lasts for 1 year, while the ministry of Jesus in the Gospel of John lasts for 3 years as evidenced by three separate Passovers in John 2:13, 6:4 and 11:55. The Jesus of the Synoptic gospels speaks only in parables (Mark 4:34, Matthew 13:34), while there are no parables in the Gospel of John.

The gospel of John also makes a very peculiar claim not found in Genesis – that there was a pre-existent Word, that the Word was God, and that the world was made through the Word. You cannot find that claim in any other gospel, nor in the Pauline epistles. The funny thing is, in early Christian literature (all the sources listed on this post are ancient sources), we do have records of heretical sects that wrote false chapters of Scripture, using the name of Jesus, and releasing his writings under the name of his apostles.

“For we know that the followers of Simon and Cleobius having composed poisonous books in the name of Christ and his disciples, carry them about for the deception of you who have loved Christ and us his servants.” (Apostolic Constitutions 6.14)

“Simon comes to do battle with us, armed with the false chapters of the Scriptures.” (Clementine Homilies: Homily III, Chapter III)

“Of whom there is one Simon, a Samaritan, whom we read of in the Acts of the Apostles, who said he was some Great Power. And among the rest of the things written in his volumes, he proclaimed as follows:
“I am the Word of God; I am the glorious one, I the Paraclete, the Almighty, I the whole of God.””(Hieronymus (In Matthaeum, IV. xxiv. 5). Text: S. Eusebii Hieronymi Comment.; Migne Patrol. Grec., VII. col. 176.)

You can make the argument that Simon Magus got some of his teachings into the canon of Christian scripture. Within the four gospels, only the 4th gospel refers to Jesus as the pre-existent Word, a distinct divine entity separate from God but also was God, through which the world was created. Similarly, the term Paraclete is only found in the Gospel of John (John 14:16, John 14:26). The other gospel authors either all suffered simultaneous amnesia when they wrote their gospels or the Jesus that they knew and believed in never made such claims.

“certain men come to Corinth, Simon and Cleobius, saying:… and that the body of man is not the creation of God; and also concerning the world, that God did not create it”(Acts of Paul VII, 1.7)

You can argue that Simon/author of the Gospel of John is saying that the world and mankind was not created directly by God, but through the Word, and the author of the non-canonical Acts wanted to stress that he’s not okay with that as it’s not stated as such in Genesis.

“He [Simon], therefore, was glorified by many as a god; and he taught that it was he himself who, forsooth, appeared among the Jews as the Son, while in Samaria he descended as the Father, and in the rest of the nations he came as the Holy Spirit.” (Irenæus (Contra Hæreses, I. xxiii. 1-4). Text: Opera (edidit Adolphus Stieren); Lipsiæ, 1848.)

“Then the Jews answered and said to Him, “Do we not say rightly that You are a Samaritan and have a demon? …Then the Jews said to Him, “You are not yet fifty years old, and have You seen Abraham? Jesus said to them, Most assuredly, I say to you, before Abraham was, I AM.” (John 8:48-57)

This is a very weird statement for the Jesus of the Book of Signs to make as the Jesus of the Synoptic gospels is supposed to a 30 year old Jew.

Insomuch as the Gospel of John is a compilation, with an opening poem (John 1:1-18), the Book of Signs (John 1:19-John 12:50), the Book of Glory (13:1-20:31), and an epilogue (John 21:1-25), it’s possible the original compiler did not realize he or she was absorbing material from other denominations of Christianity. Later redactors may have also deliberately appended sections such as the epilogue to push through their ideologies into mainstream Christianity.

“they do not know who is my precursor Simon. For if he were known, he would not be believed; but now, not being known, he is improperly believed; and though his deeds are those of a hater, he is loved; and though an enemy, he is received as a friend; and though he be death, he is desired as a saviour; and though fire, he is esteemed as light; and though a deceiver, he is believed as a speaker of truth.”(Clementine Homilies: Homily II, Chapter XVIII)

“For in the last days false prophets and corrupters shall be multiplied, and the sheep shall be turned into wolves, and love shall be turned into hate; for when Lawlessness increases, they shall hate and persecute and betray one another, and then shall appear the world-deceiver as Son of God, and shall do signs and wonders, and the earth shall be delivered into his hands, and he shall do iniquitous things which have never yet come to pass since the beginning. Then shall the creation of men come into the fire of trial, and many shall be made to stumble and shall perish” (Didache 16.3)

“And Jesus answered and said to them: “Take heed that no one deceives you. For many will come in my name, saying, ‘I am the Christ,’ and will deceive many.” (Matthew 24:4-6 NKJV)

“the prince of wickedness…fearing lest the true religion of the one and true God should be restored, hastened straightway to send forth into this world false prophets, and false apostles, and false teachers, who should speak indeed in the name of Christ, but should accomplish the will of the demon”(Recognitions of Clement: Book IV, Chapters XXXIV)