Muhammad Sadiq As-Sadr writes:

الأحوط وجوبا ترك قراءة سورة الفيل والإيلاف وكذا سورة الضحى وألم نشرح لاحتمال أن تكون سورة واحدة أو سورتين

,,According to obligatory precaution, the reading of Surah Al-Fil (105) and Al-Ilaf (106) and also Ad-Duha (93) and Alam Nashrah (94) should be refrained from, because of the possibility that they are one Surah or two Surahs.” [Manhaj-us-Salihin, Volume 1, Page 189, Number 774]

الأحوط وجوبا ترك قراءة المعوذتين في الصلاة

,,According to obligatory precaution the reading of the two supplications of refuge (113 & 114) in prayer is to be omitted.” [Manhaj-us-Salihin, Volume 1, page 196, number 814]

He is asked about this:

ذكرتم في منهج الصالحين مسألة (٨١٤): الأحوط ترك قراءة الموعوذتين في الصلاة فما هو السبب في الاحتياط برك قراءتهما وهل هو استحبابي أم وجوبي وفي كلا الصلاتين الواجبة والمستبحة؟

,,You have mentioned in Manhaj-us-Salihin, at matter 814: ﴾According to obligatory precaution, the reading of the two  supplications of refuge (113 & 114) in prayer is to be omitted.﴿ What is the reason for the precaution of omitting the reading of both and is it a desired or obligatory one and does it apply to both obligatory and desired prayer?”

To which he replies:

هذا لاحتمال كونهما ليسا من القرآن الكريم باعتبار الروايات الواردة حول ذلك وهو احتياط وجوبي وخاص بالفرائض دون النوافل

,,This is based on the possibility, that the two (113 & 114) are not part of the noble Qur’an. Taking into consideration the traditions, that came about it and it is an obligatory precaution, specifically for the obligatory prayers. Not for the voluntary ones.” [Al-Fatawa l-Khattiyyah, page 118]

Comment:

Sayyid Sadr is a great scholar recognized by the Hawzah [Here!]. The two supplications of refuge (Al-Mu’awwidhatan) are the suras Al-Falaq and Al-Nas [Here!], which Ibn Mas’ud did not see as part of the Qur’an.