Are there words other than the Basmala that the Companions were not certain were part of the Qur’an, so they refrained from writing them down, or is this an attack on the preservation of the Qur’an?

Muslims are in agreement regarding the Quran's integrity from reduction or addition, and that what was written in the Uthmani Mushaf (definition) is Quran, and what was not written therein is not. This is what the Companions and the scholars after them concurred upon. To state otherwise is considered an aspersion against the Companions and against Allah’s promise to preserve His Book: "Indeed, it is We who sent down the Dhikr (the Quran), and indeed, We will be its guardian" (Quran 15:9). The exegetes are unanimous that "the Dhikr" refers to the Quran, and that Allah preserved it from addition and reduction. The transmission of the Quran was by continuous, widespread narration (mutawatir). Therefore, the variations in readings do not affect the affirmation of a letter’s Quranic nature or its omission; whoever does not recite with a specific letter does not deny its Quranic status.