Praise be to Allah.
It is Sunnah for the worshipper to seek refuge with Allah when he comes to a verse that speaks of punishment, and to ask Him for mercy when he comes to a verse that speaks of mercy, according to the majority of scholars, because of the report narrated by Muslim (772) from Hudhayfah, who said: I prayed with the Prophet (blessings and peace of Allah be upon him) one night, and he started to recite al-Baqarah and I thought: He will bow when he reaches one hundred, but he carried on. Then I thought that he would finish it in one rak’ah, but he carried on. Then I thought he would bow after finishing it, but he started to recite al-Nisa’ and recited it all, then he started to recite Aal ‘Imraan and recited it all, reciting with a slow and measured pace. When he reached a verse that spoke of glorifying Allah, he glorified Allah; when he reached a verse that spoke of asking of Him, he asked of Him; when he reached a verse that spoke of seeking refuge with Him, he sought refuge with Him.
It was also narrated by at-Tirmidhi and an-Nasaa’i with the wording: When he came to a verse that spoke of punishment, he paused and sought refuge with Allah.
Abu Dawood (873) and an-Nasaa’i narrated that ‘Awf ibn Maalik al-Ashja‘i said: I prayed (qiyaam) with the Messenger of Allah (blessings and peace of Allah be upon him) one night. He stood up and recited Soorat al-Baqarah; he did not come to any verse that mentions mercy but he paused and asked for mercy; and he did not come to any verse that mentions punishment but he paused and sought refuge with Allah. Then he bowed for as long as he had stood, saying whilst bowing “Subhaana dhi’l-jabaroot wa’l-malakoot wa’l-kibriya’ wa’l-‘adhamah (Glory be to the Possessor of power, sovereignty, majesty and greatness).” Then he prostrated for as long as he had stood, then he said something similar whilst prostrating. Then he stood up and recited Aal ‘Imraan, then he recited the next soorah then the next.
This indicates that it is prescribed to pause when one comes to a verse that speaks of punishment and seek refuge with Allah from punishment.
An-Nawawi (may Allah have mercy on him) said in al-Majmoo‘ (3/562): ash-Shaafa‘i and our companions said: It is Sunnah for the one who recites Qur’an, in prayer or otherwise, if he comes to a verse that mentions mercy to ask Allah, may He be exalted, for mercy; if he comes to a verse that mentions punishment, to seek refuge with Allah from punishment; if he comes to a verse that mentions glorification of Allah to glorify Him; or if he comes to a verse that mentions a likeness, to reflect on it. Our companion said: That is encouraged (mustahabb) for the imam who leads the prayer, the one who prays behind an imam, and the one who prays on his own. All of that is recommended for everyone who recites Qur’an in his prayer and otherwise, whether the prayer is obligatory or supererogatory, whether he is praying behind an imam, or is leading the prayer, or is praying on his own, because it is a supplication (du‘aa’), so in all cases, they are all equal, like saying Ameen. The evidence for this matter is the hadith of Hudhayfah (may Allah be pleased with him). … This is the view of our madhhab. Abu Haneefah said: It is disliked to ask for mercy when coming to a verse that speaks of mercy, and to seek refuge with Allah during the prayer. However, our view is the view of the majority of scholars among the early generations and those who came after them.
It says in Kashshaaf al-Qinaa‘ (1/384): The worshipper may ask Allah for mercy and seek refuge with Him in obligatory and supererogatory prayers, when he comes to a verse that mentions mercy or punishment. End quote.
Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) was asked: What is the ruling on one who says Ameen, or says I seeksrefuge with Allah from the Fire, or Subhaan Allah, when the imam is reciting in a prayer in which recitation is done out loud, when the one who is praying behind him hears the verses which prompts one to seek refuge with Allah or glorify Him or say Ameen?
He replied: With regard to the verses which prompt one to glorify Allah, or to seek refuge with Him, or to ask of Him, when the reciter comes to such verses in prayer at night, it is Sunnah for him to do what is appropriate. So if he comes to a verse that contains a warning, he may seek refuge with Allah, and if he comes to a verse that speaks of mercy, he may ask Allah for it.
But if he is listening to the imam, then the best is not to be distracted by anything other than listening attentively. Yes, if it so happens that the imam pauses at the end of a verse that is a verse of mercy, and the one who is praying behind him asks Allah for mercy, or it is a verse that contains a warning and he seeks refuge with Allah, or he hears a verse that speaks of glorifying Allah, so he glorifies Him, there is nothing wrong with that. But if he does that when the imam is continuing to recite, then I am afraid that this may distract him from listening to the imam’s recitation, and the Prophet (blessings and peace of Allah be upon him) said, when he heard his companions reciting behind him during a prayer in which recitation is done out loud: “Do not do that except in the case of the Essence of the Qur’an [al-Faatihah], for there is no prayer for the one who does not recite it.”
End quote from Fataawa Noor ‘ala ad-Darb.
But some of the scholars stated that this is recommended only in the case of supererogatory prayers, because this is what is narrated from the Prophet (blessings and peace of Allah be upon him). But if someone does that in an obligatory prayer, it is permissible, even though it is not the Sunnah.
Some of the scholars said that this may be done both in obligatory and supererogatory prayers.
See the answer to question no. 85481.
And Allah knows best.