Before the final mushaf of Uthman, may Allah be pleased with him, the Sahabah had many mushafs that differed slightly; these slight differences can all be categorised in the following categories:
1- additions which were abrogated, for example the stoning verse as Yusuf mentioned
2- additions which were made as Tafsir (explanation) of the text but were not part of the Qur'an itself
3- deletions due to ignorance of their revelation, for example Ibn Mas'ud, may Allah be pleased with him, did not include the mu'awwidhatayn (the last two Surahs in him mushaf)
4. very slight differeces because of the different qira'ah
Imam Suyuti, in his Al-Itqan, mentions there is a consensus that there are 114 Surahs and the only concession is that some say anfal and tawbah (8 and 9) are one Surah so there are 113 Surahs in total.
He then goes on to mention some of the differences between the muhafs of the Sahabah. He said, regarding the mushaf of Ubayy Ibn Ka'b:
وفي مصحف أبيّ بن كعب في مصحفه فاتحة الكتاب والمعوذتين واللهم إنا نستعينك واللهم إياك نعبد وتركهن ابن مسعود
"Ubayy Ibn Ka'b included the fatihah, mu'awwidhatayn and the qunut"
He furhter goes on to exlain regarding the two "Surahs" that were revealed:
وأخرج البيهقي وأبوداود في المراسيل عن خالد بن أبي عمران أن جبريل نزل بذلك على النبي صلى الله عليه وسلم وهوفي الصلاة مع قوله {ليس لك من الأمر شيء} الآية لما قنت يدعوإلى مضر
"Al-Bayhaqi and Abu Dawud narrate that these two Surahs (the Qunut) was revealed with the verse "You have no judgement in the matter..." (3:128)"
This verse was revealed when the Prophet made du'a against the non-Muslims in Fajr and Allah told him not to do so, and with it He gave him the Qunut, which were these two Surahs.
However, later the two Surahs, which were the Qunut, to be recited in Salah (in Fajr and Witr) was abrogated and not included in the final mushaf.
This is the case with many parts of the Qur'an. It was narrated that Surah Bara'ah and Surah Ahzab were both as long as Surah Baqarah and were later abrogated to how we know it today.
The two Surahs that were abroagted still remain as the Qunut recited in Salah.
They did not pray or teach them as Qur'an or Surahs but as Du'a.
It is in Al-Bayhaqi:
وأخرج البيهقي من طريق سفيان الثوري عن ابن جريج عن عطاء بن عبيد بن عمير بن عمر بن الخطاب قنت بعد الركوع فقال: بسم الله الرحمن الرحيم اللهم إنا نستدعيك ونستغفرك ونثني عليك ولا نكفرك ونخلع ونترك من يفجرك اللهم إياك نعبد ولك نصلي ونسجد وإليك نسعى ونحفد نرجورحمتك ونخشى نقمتك إن عذابك بالكافرين ملحق
"Umar Ibn Khattab did Qunut after Ruku: ....". Therefore he did not read it as a Surah but as a Du'a.
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Here are examples of all three types:
1. the recitation is abrogated and the ruling is abrogated
This type of verse can obviously not be proven from the Qur'an since it does not exist in the Qur'an, neither as a law, nor as the Qur'an. But here is an example:
'A'isha, may Allah be pleased with her, reported that it had been revealed in the Holy Qur'an that ten clear sucklings make the marriage unlawful, then it was abrogated (and substituted) by five sucklings and Allah's apostle (may peace be upon him) died and it was before that time (found) in the Holy Qur'an (and recited by the Muslims). (Sahih Muslim)
2. the recitation remains whilst the ruling is abrogated
This means a verse is in the Qur'an which is not acted upon due to other verses. Here is an example:
The verse:
'O Prophet! We have made lawful to thee thy wives to whom thou has paid their dowers; and those whom thy right hand possesses out of the prisoners of war whom God has assigned to thee; and daughters of thy paternal uncles and aunts and daughters of thy maternal uncles and aunts, who migrated (from Makka) with thee; and any believing woman who dedicates her soul to the Prophet if the Prophet wishes to wed her; - this only for thee and not for the believers (at large);We know what we have appointed for them as to their wives and the captives whom their right hands possess; - in order that there should be no difficulty for thee and God is oft-forgiving, most merciful' (33: 50).
was abrogated by:
'It is not lawful for thee (to marry more) women after this, nor to change them for (other) wives, even though their beauty attract thee, except any thy right hand should possess (as handmaidens); and God doth watch over all things' (33: 52).
3. the recitation is abrogated whilst the ruling remains
The example for this is the stoning of the adulterer and adulteress (Mentioned in Saheeh bukhar and Saheeh Muslim )
