Some folks reading this thread saw a "Shii bias" in noticing a textual problem in this or that passage of the Qur'an; however, this is not the case. These are commonplace "textual puzzles" compiled by early scholars of the Qur'an that this Shii literature reacts to. For example..
John Wansbrough in his 𝑄𝑢𝑟'𝑎𝑛𝑖𝑐 𝑆𝑡𝑢𝑑𝑖𝑒𝑠 (1977) brings attention to a passage appended to Muqātil ibn Sulaymān’s (d. 767 CE) 𝑇𝑎𝑓𝑠𝑖̄𝑟 𝑎𝑙-𝑘ℎ𝑎𝑚𝑠𝑖𝑚ʾ𝑎𝑡 𝑎̄𝑦𝑎ℎ, which lists nine problems in total solved in quick fashion by Ibn ʿAbbās ... 
And Abū Ḥusayn al-Malaṭī (d. 987) includes a much expanded list from Muqātil on a total of 25 textual problems from the Qurʾan in his 𝑎𝑙-𝑇𝑎𝑛𝑏𝑖̄ℎ 𝑤𝑎-𝑙-𝑟𝑎𝑑𝑑. This sort of literature expands ...
menadoc.bibliothek.uni-halle.de/ssg/content/pa…
menadoc.bibliothek.uni-halle.de/ssg/content/pa…
Some early examples are lost: the grammarian Quṭrub (d. 821) wrote a treatise called 𝐾. 𝑓𝑖̄𝑚𝑎̄ 𝑠𝑎ʾ𝑎𝑙𝑎̄ ʿ𝑎𝑛ℎ𝑢 𝑙-𝑚𝑢𝑙ℎ̣𝑖𝑑𝑢̄𝑛 𝑚𝑖𝑛 𝑎̄𝑦 𝑎𝑙-𝑄𝑢𝑟ʾ𝑎𝑛 (Eng. 𝐶𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑉𝑒𝑟𝑠𝑒𝑠 𝑎𝑏𝑜𝑢𝑡 𝑤ℎ𝑖𝑐ℎ 𝑡ℎ𝑒 𝑁𝑢𝑙𝑙𝑖𝑓𝑖𝑑𝑖𝑎𝑛𝑠 𝐴𝑠𝑘).
As Quṭrub's title show, these questions are usually attributed to heretics/nullifidians, and the like (ملحدون\زنادقة). Arch-heretics whose work is lost also criticized the Qurʾan and expanded these examples—most famously Ibn al-Rēwandī in his Kitāb al-Dāmigh in the 9th century.
But insights on what such books contained can be gleaned from refutations written against them, Shii and Sunni. What is interesting to analyze is how Sunnis and Shiis answer the objections of skeptics in different ways. Here’s a famous example …
Q. Nisāʾ 4:3 is an oddly worded verse. It says, "If you (pl.) fear that you will be unjust towards orphans, then marry women who please you, be it two, three, or four." The question that many had/have was this, "What does polygyny have to do with treating orphans justly?!"
We know about the antiquity of these doubts from works like 𝑇𝑎ʾ𝑤𝑖̄𝑙 𝑚𝑢𝑠ℎ𝑘𝑖𝑙 𝑎𝑙-𝑄𝑢𝑟ʾ𝑎𝑛 of Ibn Qutaybah (d. 889), who lists it among the criticism leveled against the textual coherence of the Qur'an and its sudden shifts from topic to topic.
Ibn Qutaybah’s answer is that the connection must be found in seeing being just to orphans as akin to being just towards one’s wives (being unjust/just to enslaved consorts is not an issue for him)
The problem posed by heretics’ objection to the coherence of Q. 4:3 appears also in Shiʿite literature, in the 𝐼ℎ̣𝑡𝑖𝑗𝑎̄𝑗 of Abū Manṣūr al-Tabarsī (fl. 12th cent.) in an account of a discussion between ʿAlī ibn Abī Ṭālib and a zindīq, who says doubts prevent his belief
ʿAlī’s response (according to this account at least) to the man’s criticism of the coherence of Q. 4:3 is extraordinary: The problem, he says, is due to the poor job that ʿUthmān and the others did while compiling the Qurʾan, what he calls 𝑖𝑠𝑞𝑎̄𝑡̣ 𝑎𝑙-𝑚𝑢𝑛𝑎̄𝑓𝑖𝑞𝑖̄𝑛
... 𝑚𝑖𝑛 𝑎𝑙-𝑞𝑢𝑟ʾ𝑎̄𝑛. Between the statement regarding treating orphans justly and the statement regarding polygyny, ʿAlī continues, is a full third of the Qurʾan (lost?). It's the same problem is being addressed, but it's answered with a different theological paradigm.
