Ahadith that Contradict the Quran

Most blessed is He who revealed to His servant the Criterion of right and wrong so that it might be a warning to the entire world. (25:1)

These are the verses of God We convey to you with truth. Then, in what HADITH, if not in God and His verses, will they believe? (45:6)

Not all the ahadith contradict the Qur'an directly - some contradict the general injunction in 16:116 (Do not keep uttering in falsehood, "This is lawful and this is unlawful”, thus inventing lies against God. Those who fabricate lies against God, fail to prosper in their own ‘self’) and create commandments not found in the Qur'an, or extend or nullify Qur'anic commandments.

Guidance

Hadith

Narrated Tariq: `Abdullah said, "The best talk is Allah's Book (Qur'an), and the best guidance is the guidance of Muhammad." (Sahih al-Bukhari 6098)

Qur'an

We obey You alone and we ask You alone to help us. Guide us to the straight path (1:4-5)

... God shows the lighted road to those who would acknowledge the truth and thus resolve their disputes. And God guides to the straight road him who wills to be guided. (2:213)

Surely, you cannot guide everyone you love, but it is God Who guides him who wishes to be guided. And He is best Aware of those who will be rightly guided. (28:56)

The Testimony (Shahadah)

Compulsion in Religion

Sects

Apostasy

Knowledge of the Future

Miracles of Prophet Muhammad

Loving Prophet Muhammad

Superiority of Prophet Muhammad

Prophet Muhammad as enforcer

The Prophet Bewitched

Age of Marriageability

Punishment for Adultery

Dogs are to be Killed

The Second Coming of Jesus

Women are the Lesser Gender

Covering the Faults of Others

The Best Deeds

Deeds are not (really that) Important

Idols Worshipped by Others

Blood of a Disbeliever

Intercession on Judgment Day

Prohibited Foods

Performing Rites on Behalf of Others

What Constitutes Major Sins

But there are hundreds, if not thousands of hadith that do not directly contradict the Qur'an, but are not rational, display no mercy, or justice, or compassion etc etc...

For example, does the mi'raj hadith directly contradict Qur'an? To me it's mainly illogical for a number of reasons — does Musa know the capacity of God's creation better than Him? Is it realistic for a prophet to bargain with God?

Do not confound the truth with falsehood, nor conceal the truth while you are well aware of it. (2:42)