The text of The Qur'an has a few unfortunate problems. The first is that the Suras are ordered roughly in size order, because the original compilers didn't know when each was dictated. This is important because older verses can be overridden by new ones. Secondly, there could be any quantity of missing text, potentially including important declarations, or important nullifications of other statements. Thirdly, the amount of variant and contradictory collections of Suras in the 650s1 worried the first caliphs into creating a final version - it was they, and not Muhammad, who put the Qur'an together2,3, Although their methods were sensible, there was no sure way to know which versions of texts to dismiss and which to include; the compilation process was all too human, and it is undoubted that at least some mistakes were made. Fourthly, the verses that Muhammad said were inserted into the scripture by Satan - the Satanic verses. These verses pacified three hostile pagan neighbours by saying that their gods were valid. If this is true, then Satan saved Muhammad's life, and the Qur'an in total is indebted to Satan. Or, if false, they were actually invented by Muhammad to save himself. In either case, we don't know how many other verses are untrustworthy.
The Qur'an was revealed to Muhammad and he transmitted it to his following, who then compiled it in the decades after his death. Varied compilations of fragments of "the recital" were created in the mid 650s1. There were multiple compilations at the time, each using different material based on the recitations of different caliphs. This variation caused concern for Muslim scholars at the time. 'We thus face serious contradictions in our source material regarding two issues: who collected the Qur'an, and what it was collected from. In historical terms, the differences between the rival accounts are not trivial'4. In the tenth century there were between 7 and 14 major different versions of the Qur'an available5.
“When the Prophet died in 632, ten years after he migrated from Makkah to Madinah, the Quran was scattered in fragments and in partial private collections written on stones, bones, palm leaves and skin parchments. Private collections varied in length, form, and content. Minor, but often significant variations in the reading of certain words or phrases existed as well. These variant readings persisted and finally became identified with specific Qur'an readers of the first and later generations of Muslim scholars. As Islam spread beyond Arabia, major disagreements in reading and actual grammatical mistakes by reciters led to a call for an official collection to be used throughout the Islamic domains.
This task may have been initiated by Abu Bakr, the first caliph or successor to the Prophet as head of the Muslim community. Abu Bakr is said to have been motivated by the deaths of many Quran reciters in the wars of apostasy. [...] The death of a large number of oral transmitters of the Quran could have resulted in the loss or grave distortion of the sacred text.”
Upon the compilation of the version we have today there were doubts and the writing of Muslim scholars expressed it: That some of the text may have been missed. This was why the compilations were completed in the first place, because those who Muhammad had instructed the words of the angel Gabriel to were becoming old. Early Muslim sources state '[A Koran compiler's] Koran was incomplete, perhaps dramatically so. 'Let none of you say', averred the pious son of Caliph Umar, 'that he has the whole Koran in his possession. How does he know what the whole of it is? Much of the Koran has gone'4, and early compilers also despaired 'of the sharp divergences in Koranic recitation that had appeared among the Muslims - just had been the case, he warned, among the Jews and Christians before them'4. Umar was the second caliph (leader of Muslim community); yet despite his concerns he did not collect the parchments, stories and sayings of the Prophet into an authoritive compilation.
“Although the first two caliphs, Abu Bakr and 'Umar were concerned about the possibility of the loss of revelation by the deaths of men and women who had memorized portions of it, it was not until the third caliph 'Uthman, that all the materials were gathered together to produce a standard written text. This was completed by 650 and all subsequent Qur'ans reflect this text.”
Not only is the Qur'an is incomplete (there are rules, guidelines and comments by God that we no longer possess), but also it is not compiled in order. The order of texts is important because earlier rulings are overruled by later ones, and sometimes this has happened on rather important topics. But it was not possible for the patchwork canonisation to be done chronologically. We do not know what order the texts were supposed to be in6.
Islam does not only rely on canonical texts. The Hadith sayings are given religious authority and attributed to Muhammad:
“Modern Western scholarship, however, examining critically the earliest surviving documents, has cast a much more fundamental doubt over the Hadith literature. The first to raise questions about the traditional version of the rise of the Hadith literature was Ignaz Goldziher. He showed that up to three centuries after Muhammed, many individuals, political parties and sectarian movements within Islam were manufacturing Traditions that supported their claims and positions. These Traditions, claiming to be on the authority of Muhammed, gave each faction legitimacy and authenticity.”
It is clear that Islam has serious issues with its texts. Historically, Muslim scholars have known this:
“...[critics say] that the Koran often copied Biblical stories, and sometimes did so inaccurately [...]. Against the charge that Muhammad had copied from previous scriptures Muslims developed the doctrine of Muhammad's illiteracy, which implied his complete inability to read the scriptures. The doctrine was based on the application to Muhammad in the Koran of the adjective ummì. which was alleged to mean 'illiterate'. The word occurs a number of times in the Koran in both singular and plural, and appears to have been taken from the Jews and to mean 'Non-Jewish' or 'Gentile' or 'unscriptured'.”
"Islamic Fundamentalism and Modernity" by Montgomery Watt (1989)8
The Qur'an is very poor at story-telling. Subtleties, ramifications and lessons are all left completely unexplained, so that within a generation or two of being written, many aspects of the meaning of stories have been lost. It makes the reading quite unsatisfactory. The Qur'an is good at making statements about god, destiny and duty, but completely inadequate at teachings morals or goodness. Its history reads like half-remembered summaries of various unconnected events.
The whole Qur'an could be summarized into a series of no more than 50 statements. These are merely repeated continuously throughout most the Qur'an. Its strength is the clarity and coherence of these statements. Its weakness is the occasional foray into stories and myths, poorly told, with almost no moralizing even about horrendous acts, and a lack of continuity of meaning.
At one point Muhammad and his kin were opposed by the polytheists around them. In particular, they were oppressed by the followers of 3 pagan gods in Mecca. When defeated, surrounded and under siege, Muhammad 'seems to have even compromised his monotheism, at first, to make peace with the Meccans'10 and then he suddenly recalled some text that stated that the three pagan gods were valid intercessors after verses 19 and 20 (see how it reads now: Qur'an 53:10-12,18-23), after all! Lucky for Muhammad he remembered this important fact!
When Muhammad had a powerful army and his exiled followers returned, he recited a further passage: saying that it was an error, the three pagan gods were not valid - that Satan recites his own verses but now that "God annuls what Satan casts" Qur'an 22:52! The same in Qur'an 16:101-103, where it says some verses can be later changed for others by God - and here also, the authors must have known how dodgy it sounds, as it mentions that these abrogations cause people to cry out "you are only a forger!". But how can this be, when Qur'an 39:28 says that the Qur'an is perfect? If it's perfect, it's not possible to update verses with a better version - this can only mean that those verses weren't perfect. Whether it was Muhammad changing things, or Satan, or the Angel Gabrielle himself, it undermines our trust in the entire book. If that insertion was made, but annulled, what others have been made, and left in?
It seems that Muhammad was defeated and gave in to pressure from his enemies. He compromised truth, God's eternal word, for material benefits: to stay alive. This is the truth of the matter. If Muhammad can do this here, he could have done it with any part of the Qur'an. We do not know which parts of the text were due to Muhammad's materialism and selfishness and which parts he honestly thought were the words of Gabriel. Like the Christian scriptures, we are left only with Human text, not Godly text.
Islamic tradition has it that these verses were not the result of Muhammad's insincerity. They were sneaked into the Qur'an by Satan. At an emotional moment Satan tricked Muhammad into thinking that these verses were genuine, and it was only later that "God annuls what Satan casts" (Qur'an 22:52).
“Muslims have always been uncomfortable with this story, unwilling to believe that the Prophet could have made such a concession to idolatry. [...] It seems unthinkable that such a story could have been invented by a devout Muslim such as al-Tabari [...]. Besides, it explains the fact why those Muslims who had fled to Abyssinia returned: they had heard that the Meccans had converted. It seems apparent that this was no sudden lapse on the part of Muhammad, but had been carefully calculated to win the support of the Meccans. It also casts serious doubts on Muhammad's sincerity: Even if Satan had really put the words in his mouth, what faith can we put in a man so easily led astray by Satan? Why did God let it happen? How do we know there are no other passages where Muhammad has not been led astray?”
Which leaves us with some very interesting problems! If Satan can inspire verses then we do not know which ones are valid and which ones are not. For all intents and purposes, the faked ones were real from the time Satan slipped them in until the time God annulled them. A period of some years! What further verses is God to cancel? What other verses were inspired by Satan? We do not know, so the Qur'an cannot be trusted.
The Muslim world has never (apparently!) produced any critical analysis of the texts of the Qur'an and the Hadiths, in the manner of serious academic investigation to its sources and generation - what is called "Higher Criticism". There is lots of Arabic commentary on the sources, oral transmission, and respectability of individual verses and hadiths and this is invaluable, but, all of them are from the point of view that the canon is holy. Their starting point is literalist and accepting, rather than neutral. Because of their conclusions, all of the scholars that we know about who ventured forth with impartial analysis have been shunned, punished, silenced and even when they have fled their countries of origin, have found themselves harassed even in Western countries. It sometimes feels as if Western scholars are going to have to do the entire historical analysis themselves, but relying on the most fragmentary historical data (as most of the evidence is lost).
“Higher Critical scholarship of the Koran, using methodologies adapted from biblical criticism, is still largely confined to scholars working in Western universities. So sensitive is this area for Muslims that 'Ibn Warraq', a Muslim-born writer trained in Arabic who accepts the findings of radical Western scholarship, has felt it necessary to publish his work under a pseudonym. [...] The Egyptian academic Nasr Abu Zaid, who ventured to use modern literary critical methodology in his approach to the Koran, was forced into exile. Higher criticism of the Koran, where the text is deconstructed in accordance with methods developed by biblical analysts since the 18th century, is still very largely confined to scholars who are not Muslims. Examples include the work of John Wansbrough, Patricia Crone, and Gerald Hawting, Western scholars of Islam who do not accept the traditional view of its origins as related in the earliest texts.”