It is always good as well as relevant to be aware of some of the apparent discrepancies found in the narration of the Gospel of John.
John 5: 4, is absent in some of the important ancient manuscripts. So also, the passages in John 7: 53 – 8: 11. Hence some consider these as secondary and give them only in the footnotes.
The presence of verses 6-8 and 15 in the prologue of John 1: 1-18 seems to interrupt the flow of the text as these verses introduce John the Baptist, while the rest of the prologue is on Jesus, the Word.
In John 3, the text is interrupted by John 3: 22-30, which is a tradition about John the Baptist and can very well fit into John 1: 19-34. Moreover, if John 3: 21 is followed by John 3: 31, the flow in the narration is uninterrupted.
John 7: 15-24, speaks about the violation of Sabbath. Thematically this seems out of place while it suits very well in John 5, where Jesus reveals the meaning of authentic Sabbath.
John 12: 44, reports: “Then Jesus cried aloud”. This is the introduction to a central summary of the Gospel message. But this seems to be in discrepancy with John 12: 36: “After Jesus had said this, he departed and hid from them”.
John 14: 31, reads: “Rise, let us be on our way”. It is an invitation for spatial movement. However, the actual movement of Jesus according to this instruction is only in John 18: 1. John 15: 1-17, 26, is the continuation of Jesus’ discourse and prayer. So John 14: 31, seems to be misplaced.