Ibn Warraq a noted writer on the Koran and publisher of scientific research on it writes in his book ‘What the Koran Really says’:
“Contradictions do abound in the Koran, and the early Muslims were well aware of them; indeed they devised the science of abrogation to deal with them”.
“According to this doctrine, certain passages are abrogated by verses revealed afterwards, with a different or contrary meaning”
Muslims claim that the Koran is the actual word of God, and that it was transmitted to Muhammad by the angel Gabriel in dreams or visions. From this Muslims believe that the Koran is perfect as a scripture, not only as far as its literary quality is concerned but also as far as the correctness of its statements go.
The Koran itself claims that it is free of inconsistency. See Koran 4.82:
..If it had been from other than Allah they would have found in it much inconsistency.
Maulana’s comment on 4.82 reinforces the claimed absence of discrepancy in the Koran. He says:
“A clear proof of the Quran being the Divine Book is that none of its statements contradict any established truth. It does not contain anything which is against human nature. It does not conflict with any facts known throughout the earlier divine books. There is no sign of any part of its content contradicting any fact verified by the body of knowledge established by observation and experimentation. The Quran’s total conformity with factual realities is the definite proof that it uis the message revealed by God. The Quran being free from contradictions will appear as such to one who ponders over the matter. For truth to appear as truth depends on the sincerity with which one tries to understand it, but one who does not ponder over it will ceaselessly raise baseless objections against this Book..”
Maulana speaks as one who is committed to seeing nothing imperfect in the Koran. It is important for Muslims that the Koran is perfect as how otherwise would a text which was obviously not perfect command belief in it as the word of God.
Some statements which are obvious mistakes in the light of scientific knowledge also stand out but these are considered in a later chapter. Others are simply bizarre or mythological. These also will be considered later.
Other imperfections – such as contradictions – stand out so clearly that Muhammad himself had to contend with them. The doctrine of abrogation was devised specifically for this purpose and itself depends on authority of the Koran. This chapter focuses on how Islam deals with the contradictions which occur frequently in the Koran and raises the question whether contradictions are compatible with the claimed divine authorship of the Koran.
The Koran itself addresses the problem when it asserts that it was well within the power of God, to replace one verse with another. Sura 2.106 makes this clear:
“Nothing of Our revelation (even a single verse) do we abrogate or cause to be forgotten, but We bring (in place) one better or the like of it. Do you not know that Allah is able to do all things?”
Maulana understands this verse in his commentary as referring to the Koran changing earlier scriptures for the better, but others use 2.106 to justify abrogations of earlier Koranic verses by later ones.
Under this doctrine of abrogation verses delivered later in Muhammad’s ministry are to be preferred to those delivered earlier, as Allah has later replaced earlier ones with better ones. However the task of identifying abrogating verses is none too easy and traditional scholars themselves disagree how many verses have been abrogated. The Wikislam website offers a list of abrogated verses. The verse of the sword 9.5 (…Slay the idolaters wherever you find them.. ) is said to have abrogated about 113 other more peaceful verses alone. The task is not made any easier by the fact that the Koran is not set out chronologically, but generally with the longer Suras placed first and the shorter ones at the end.
The Traditional Islamic viewpoint is that the Koran is perfect. This is a central belief upon which Muslim acceptance of the authority of the Koran is based. Muslims therefore tend to deny, explain away or close their eyes to the Koran’s defects, whether clear contradictions, scientific errors, incredible and mythological stories or other inconsistencies. Indeed as we see in a later chapter Islamic Tradition claims the Koran is an unequalled masterpiece.
From a common sense viewpoint it will be queried why the all-knowing God has the need to change his mind at all, when delivering revelation to humankind. Surely an all-knowing and wise God would deliver one set of perfect revelations which would anticipate all eventualities. By handing down first one revelation but then changing it on second thoughts (either in the same scripture or in successive ones), is not God demonstrating a rather human failing, not to be expected of his divine nature? To assert that it is within the power of God to change his mind does not really deal with the challenge that an all seeing and knowing God would not need to change his mind. Changing one’s mind is a feature of the human mind.
An analysis of every contradiction in the Koran would be the subject of a book in its own right. In the next three sections further examples are given.
 What the Koran really says” ed Ibn Warraq p67
 Ibid p68
 Pickthall translation
 See Farooq Ibrahim’s discussion of this on http://www.answering-islam.org/Authors/Farooq_Ibrahim/abrogation.htm
 See the discussion in http://www.answering-islam.org/Quran/abrogatedverses.html