In the course of Jesus’ farewell discourse, he says some things that can be difficult for us to wrap our minds around. One of the more difficult portions of the discourse to clearly grasp is Jesus’ teaching on the convicting work of the Holy Spirit in John 16:8-11. The economy of language that Jesus uses, combined with the variety of possible meanings or nuances available for each of the few words used, means that much ink has been spilled in trying to understand that aspect of the Spirit’s work.
But the reality is that even before we get to vv8-11, Jesus makes a challenging statement. Just a few verses prior, he says, “But now I am going to him who sent me, and none of you asks me, 'Where are you going?' 6 But because I have said these things to you, sorrow has filled your heart” (John 16:5-6 ESV). Now, the astute Bible reader will know that Peter actually asked that exact question at the beginning of the farewell discourse. In John 13:36 (ESV), we read, “Simon Peter said to him, ‘Lord, where are you going?’ Jesus answered him, ‘Where I am going you cannot follow me now, but you will follow afterward.’” Just to be clear, the exact words are used in both John 13:36 and John 16:5, so we are not dealing with a similar kind of question but the exact same question.
To (over)simply things, we’re faced with two options. Either we assume that John was a bad editor and had a poor memory—and that every early copier of John’s gospel was too timid to speak up about the contradiction—or we affirm the inerrancy of the Scriptures and seek to understand how these two data points might fit together.
With respect to reconciling this apparent contradiction, D.A. Carson’s thoughts are worth presenting in full:
One suspects that part of the problem lies in a fairly mechanical approach to the text, an approach that is sometimes insensitive to literary nuances. In the flow of the argument both in 13:36 and in 14:5, it is not clear that either Peter or Thomas was really asking the question formally represented by their words. A little boy, disappointed that his father is suddenly called away for an emergency meeting when both the boy and his dad had expected to go fishing together, says, ‘Aw, Dad, where are you going?’, but cares nothing at all to learn the destination. The question is a protest; the unspoken question is ‘Why are you leaving me?’ The disciples have been asking several questions of that sort; they have not really asked thoughtful questions about where Jesus is going and what it means for them. They have been too self-absorbed in their own loss. Moreover the drift of all four Gospels assures us that none of the inner ring of disciples entertained the idea, before the cross, that the Messiah would simultaneously be conquering king, suffering, dying servant and resurrected Lord. So how much of Jesus' talk about his departure to the Father did they understand at this point?
One benefit of Carson’s comments is that we are reminded how our words can mean very little. In certain contexts, saying to someone else, “We should get together soon,” does not actually mean that we should get together soon. Or, more frequently perhaps, when someone asks, “How are you?”, that person very well may not intend to be inquiring into your health and general state of being. In fact, when we take statements or questions like these literally, we’re the ones who transgress the cultural norm and make things awkward (a habit I confess that I have!).
Returning to a resolution of the apparent contradiction, it is helpful to remember that Peter’s question comes in the form of an outburst, an interruption at the very beginning of the farewell discourse. That observation makes it much more likely that his words are really conveying a protest against the implications of the speech that Jesus had just begun. We should also remember that tension had likely been building towards the end of Jesus’ ministry. Matthew, Mark, and Luke remind us that Jesus foretold his death and resurrection, but Carson reminds us that what that really meant could only be understood by the disciples after the resurrection and the sending of the Holy Spirit. For these reasons, it is not all that contradictory for Jesus to say that nobody was really asking the right question, even if the form of the question had already been asked, because there was much missing that needed to be pieced together.
 D. A. Carson, The Gospel According to John (Grand Rapids: Eerdmans, 1991), 533.