Problem: John writes, “I had many things to write to you, but I am not willing to write them to you with pen and ink; 14 but I hope to see you shortly, and we will speak face to face” (3 Jn. 13). Catholic apologists claim that this implies that oral tradition is greater than written Scripture.
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Problem: John writes, “Diotrephes, who loves to be first among them, does not accept what we say. 10 For this reason, if I come, I will call attention to his deeds which he does, unjustly accusing us with wicked words; and not satisfied with this, he himself does not receive the brethren, either, and he forbids those who desire to do so and puts them out of the church” (3 Jn. 9-10). John seems to be against Diotrephes engaging in church discipline here, but the rest of Bible speaks about this practice (Mt. 18:15-17; 1 Cor. 5:1-13; 2 Thess. 3:6). Does the Bible support church discipline or not?
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Problem: John writes, “The elder to the chosen lady and her children, whom I love in truth” (2 Jn. 1). Who was this “lady,” and why was he writing that he loved her? Did John have a romantic relationship with this woman?
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Problem: John writes, “This is the true God and eternal life” (1 Jn. 5:20). But what does the “this” refer to? Does it refer to Christ? Or does it refer the Father?
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Problem: How many Gods are there, one or many?  The Bible speaks of both one and many.  There is only one God in actuality, but there are many false gods that idolators believe in.
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Problem: The Bible tells us that God both loves people and hates people. Whether we like it or not the Scriptures teach that God hates those who love violence and love evil. God is too holy to approve of those who love what is opposite to God’s character and nature. But on the other hand, generically speaking, God loves the whole world (John 3:16). Also, he lets the sun shine on the good and the bad. He let’s the rain fall upon all people. So, in this context, he loves all (Matthew 5:43-48).
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Problem: John writes, “Everyone who hates his brother is a murderer; and you know that no murderer has eternal life abiding in him” (1 Jn. 3:15). Are murderers not forgiven by the blood of Christ?
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Problem: The Bible says both to hate and to not hate. So which is it? The solution is found in the context of different statements regarding hate.  In one sense Jesus uses hyperbole to emphasize how important he is compared to all others and in another sense, were to love our brothers in Christ.
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Problem: Some verses seem to say that a Christian cannot sin, but others are clear that, while Christians ought not to sin, they still do. Is this a contradiction? How do we reconcile these verses? Can a Christian sin and still be Christian?
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Problem: John writes, “No one who abides in Him sins; no one who sins has seen Him or knows Him… 8 the one who practices sin is of the devil; for the devil has sinned from the beginning. The Son of God appeared for this purpose, to destroy the works of the devil. 9 No one who is born of God practices sin, because His seed abides in him; and he cannot sin, because he is born of God” (1 Jn. 3:6, 8-9). Does this mean that Christians cannot sin?
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Problem: Some interpreters claim that we do not need Bible study or instruction from fellow Christians, because we are each individually instructed by the Holy Spirit. This is why Paul writes, “You have no need for anyone to write to you” (1 Thess. 4:9) and why John writes, “You have no need for any­one to teach you” (1 Jn. 2:27). Is this the case?
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Problem: John writes, “[Jesus] is the propitiation for our sins; and not for ours only, but also for those of the whole world” (1 Jn. 2:2). However, regarding 1 John 2:2, Calvinist James Montgomery Boice writes,

John may be stressing the universal application of Christ’s work. Since ‘sacrifice of atonement’ is a strongly Jewish term and something associated in Jewish minds with the propitiation made at the temple on the Day of Atonement, John may be saying, ‘Jesus made propitiation for our sins; but not just the sins of us who are Jews, which we might think since atonement is a Jewish tradition, but for all the peoples of the world. In that sense, he is a universal Savior.’[1]
Steele and Thomas write,

One reason for the use of these expressio–ns was to correct the false notion that salvation was for the Jews alone… These expressions are intended to show that Christ died for all men without distinction (i.e., He died for Jews and Gentiles alike) but they are not intended to indicate that Christ died for all men without exception (i.e., He did not die for the purpose of saving each and every last sinner).[2]
John Piper writes,

The ‘whole world’ refers to the children of God scattered throughout the whole world.[3]
Thus five point Calvinists argue that this passage refers to ethnic universality—not individual universality.
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