Mawdudi in his commentary said:

Question whether Mu’awwidhatayn are, or are not, Quranic

The above discussion is enough to help one understand fully the theme and content of the two Surahs, but since three points in the books of Hadith and commentary concerning these Surahs have been discussed, which are likely to create doubts in the minds, it is necessary to clear them also here.

First, whether it is absolutely established that these two Surahs are the Qur’anic Surahs, or whether there is some doubt in this regard. This question arose because in the traditions related from an illustrious Companion like Hadrat Abdullah bin Mas’ud, it has been said that he did not regard these two Surahs as the Surahs of the Qur’an and had eliminated these from his copy of the Mushaf. Imam Ahmad, Bazzar, Tabarani, Ibn Marduyah, Abu Ya’la, Abdullah bin Ahmad bin Hanbal, Humaydi, Abu Nu’aim, Ibn Hibban and other traditionists have related this from Hadrat Abdullah bin Mas’ud with different chains of transmitters and mostly on sound authority. According to these traditions, he not only eliminated these Surahs from the Mushaf but it has also been reported that he used to say: “Do not mix up with the Qur’an that which is not of the Qur’an. These two Surahs are not included in the Quran. This was only a command enjoined on the Holy Prophet (sallalahu alayhi wa ala alihi salam) for seeking God’s refuge.” In some traditions there is also the addition that he did not recite these Surahs in the Prayer.

On the basis of these traditions the opponents of Islam had an opportunity to raise doubts about the Qur’an, saying that this Book, God forbid, is not free from corruption. For when, according to a Companion of the rank of Hadrat Abdullah bin Mas’ud, these two Surahs are an annexation to the Qur’an, many other additions and subtractions also might have been made in it. To rid the Qur’an of this blame Qadi Abu Bakr Al-Baqillani, Qadi Iyad and others took the stand that Ibn Mas’ud was not in fact a denier of the Mu’awwidhatayn being Qur’anic but only refused to write them in the Mushaf. For, according to him, only that which the Holy Prophet (sallalahu alayhi wa ala alihi salam) had allowed, should be written in the Mushaf, and Ibn Mas’ud did not receive the information that the Holy Prophet had allowed this. But this stand is not correct, for according to sound evidence, it is confirmed that Ibn Mas’ud (may Allah be pleased with him) had denied that these were Surahs of the Qur’an. Some other scholars, for instance, Imam Nawawi, Imam Ibn Hazm and Imam Fakhr-ud-din Razi, regard this as a pure lie and falsehood that Ibn Mas’ud had asserted any such thing. ………

Now, the question is: How can the blame that attaches to the Qur’an because of these traditions of Ibn Mas’ud correctly refuted? This question has several answers which we shall give below in sequence:

1.Hafiz Bazzar after relating these traditions of Ibn Mas’ud in his Musnad, has written that he is solitary and isolated in his this opinion; no one from among the Companions has supported this view.
2. The copies of the Qur’an which the third Caliph, Hadrat Uthman (may Allah be pleased with him), had got compiled by the consensus of the Companions and which he had sent from the Islamic Caliphate officially to the centers of the world of Islam contained both these Surahs.
3.The Mushaf which, since the sacred time of the Holy Prophet (sallalahu alayhi wa ala alihi salam) till today, has the seal of consensus of the entire world of Islam, contains both these Surahs. The solitary opinion of only Abdullah bin Mas’ud, in spite of his high rank, has no weight against this great consensus.
4. It is confirmed by sound and reliable ahadith from the Holy Prophet (sallalahu alayhi wa ala alihi salam) that he not only recited these Surahs in the Prayer himself but instructed others also to recite them, and taught them to the people as the Surahs of the Qur’an. Consider, for instance, the following ahadith:

We have cited on the authority of Muslim, Ahmad, Tirmidhi and Nasai the tradition of Hadrat Uqbah bin Amir that the Holy Prophet told him about Surah Al-Falaq and Surah An- Nas, saying that those verses had been revealed to him that night. A tradition in Nasai from Uqbah bin Amir is to the effect that the Holy Prophet (sallalahu alayhi wa ala alihi salam) recited both these Surahs in the Morning Prayer. Imam Ahmad on sound authority has related in his Musnad the tradition from a Companion that the Holy Prophet said to him, “When you perform the Prayer, recite both these Surahs in it.”

In Musnad Ahmad, Abu Daud and Nasai this tradition of Uqbah bin Amir has been related: “The Holy Prophet said to him: Should I not teach you two such Surahs as are among the best Surahs that the people recite? He said: Do teach me, O Messenger of Allah. Thereupon the Holy Prophet taught him the Mu’awwidhatayn. Then the Prayer began and the Holy Prophet recited the same two Surahs in it also, and when after the Prayer the Holy Prophet passed by him, he said to him, ‘O Uqbah, how did you like it?’ Then he instructed him to the effect: When you go to bed, and when you get up from bed, recite these Surahs.”

In Musnad Ahmad, Abu Da’ud, Tirmidhi and Nasa’i there is a tradition from Uqbah bin Amir, saying that the Holy Prophet exhorted him to recite the Mu’awwidhat (i.e. Qul Huwa Allahu ahad and the Mu’awwidhatayn) after every Prayer.

Nasai, Ibn Marduyah and Hakim have related this tradition also from Uqbah bin Amir: “Once the Holy Prophet was riding on a conveyance and I was walking along with him with my hand placed on his sacred foot. I said: Kindly teach me Surah Hud or Surah Yusuf. He replied: In the sight of Allah there is nothing more beneficial for the servant than Qul a’udhu bi-Rabbil-falaq.”

A tradition from Abdullah bin Abid al-Juhani has been related by Nasai, Baihaqi and Ibn Sad, saying that the Holy Prophet (sallalahu alayhi wa ala alihi salam) said to him: “Ibn Abid, should I not tell you what are the best things out of the means by which the seekers of refuge have sought refuge with Allah? I submitted: Do teach me, O Messenger of Allah. He replied: Qul a’udhu bi-Rabbil- falaq and Qul a-udhu bi Rabbin-nas – both these Surahs.”

Ibn Marduyah had related from Hadrat Umm Salamah: “The Surahs best liked by Allah are: Qul a’udhu bi-Rabbil-falaq and Qul a’udhu bi-Rabbin-nas.”

Here, the question arises: what caused Hadrat Abdullah bin Mas’ud the misunderstanding that these two are not Surahs of the Qur’an? We get the answer to it when we combine two traditions: first, that Hadrat Abdullah bin Mas’ud asserted that this was only a command which the Holy Prophet (sallalahu alayhi wa ala alihi salam)was given to teach him the method of seeking refuge with Allah; second, the tradition which Imam Bukhari has related in his Sahih, Imam Ahmad in his Musnad, Hafiz Abu Bakr al- Humaidi in his Musnad, Abu Nu’aim in his Al-Mustakhraj and Nasai in his Sunan, with different chains of transmitters, on the authority of Zirr bin Hubaish, with a slight variation in wording from Hadrat Ubayy bin Kab, who held a distinguished place among the Companions on the basis of his knowledge of the Qur’an. Zirr bin Hubaish states: “I said to Hadrat Ubayy: Your brother, Abdullah bin Mas’ud, says these things. What do you say about this view? He replied: I had questioned the Holy Prophet (upon whom be peace) about this. He said to me: I was told to say ‘qul’, so I said ‘qul’. Therefore, we too say the same as the Holy Prophet said.”

In the tradition related by Imam Ahmad, Hadrat Ubayy’s words are to the effect: “I bear witness that the Holy Prophet (sallalahu alayhi wa ala alihi salam) told me that Gabriel (peace be on him) had told him to say: Qul a’udhu bi-Rabbil-falaq; therefore, he recited likewise, and Gabriel asked him to say: Qul a’udhu bi- Rabbin-nas; therefore he too said likewise. Hence, we too say as the Holy Prophet said.” A little consideration of these two traditions will show that the word qul (say) in the two Surahs caused Hadrat Abdullah bin Mas’ud the misunderstanding that the Holy Prophet (upon whom be peace) had been commanded to say: A’udhu bi-Rabbil-falaq and A’udhu bi-Rabbin-nas. But he did not feel any need to question the Holy Prophet about it. In the mind of Hadrat Ubbay bin Kab also a question arose about his and he put it before the Holy Prophet. The Holy Prophet replied: “Since Gabriel (peace be on him) had said qul, so I too say qul.” Let us put it like this. If somebody is commanded and asked: “Say, I seek refuge”, he will not carry out the command, saying: “Say, I seek refuge”, but he will drop the work “say” and say: “I seek refuge.” On the contrary, if the messenger of a superior officer conveys to somebody the message in these words: “Say, I seek refuge”, and this command is given to him not only for his own person but to be conveyed to others, he will convey the words of the message verbatim to the people, and will not have the permission to drop anything from the text of the message. Thus, the fact that these two Surahs begin with the word qul is a clear proof that it is Divine Word, which the Holy Prophet (sallalahu alayhi wa ala alihi salam) was bound to convey verbatim. It was not merely a command given to him for his person. Besides these two Surahs, there are 330 other verses in the Qur’an which begin with the word qul (say). The presence of qul in all these is a proof that it is Divine Word. which was obligatory for the Holy Prophet to convey verbatim; otherwise if qul everywhere had meant a command, the Holy Prophet would have dropped it and said only that which he was commanded to say, and it would not have been recorded in the Qur’an, but, on the contrary, he would have remained content with saying only what he was commanded to say.

Here, if one considers this, one can understand fully well how unreasonable it is to regard the Companions as infallible and to make the clamor that a Companion has been defamed as soon as one hears a saying or doing of his being described as wrong. Here, one can clearly see what a blunder happened to be committed by an illustrious Companion like Hadrat Abdullah bin Mas’ud about two Surahs of the Qur’an. If such an error could be committed by an eminent Companion like him, others also might commit an error. We can examine it in the scientific way, and describe it as wrong if a thing said or done by a Companion is proved to be wrong. But wicked indeed would be the person who went beyond describing a wrong act as wrong and started reproving and finding fault with the Companions of the Holy Prophet of Allah (sallalahu alayhi wa ala alihi salam). Concerning the Mu’awwidhatayn the commentators and traditionists have described the opinion of Ibn Mas’ud as wrong, but no one has dared to say that by denying these two Surahs of the Qur’an, he had, God forbid, become a disbeliever.(end of quote).