Part 1 ....
Allah, Adam, and the Angels. There are a great number of problems and inconsistencies between the several accounts of Adam's creation, Allah's command to prostrate before Adam, Satans refusal, etc.
#1.
Can Allah be seen and did Muhammad see his Lord? Yes [S. 53:1-18, 81:15-29], No [6:102-103, 42:51].
Were Warners Sent to All Mankind Before Muhammad? Allah had supposedly sent warners to every people [10:47, 16:35-36, 35:24], Abraham and Ishmael are specifically claimed to have visited Mecca and built the Kaaba [2:125-129]. Yet, Muhammad supposedly is sent to a people who never had a messenger before [28:46, 32:3, 34:44, 36:2-6]. This article also raises other issues: What about Hud and Salih who supposedly were sent to the Arabs? What about the Book that was supposedly given to Ishmael? Etc.
Can Angels Cause the Death of People? The Qur'an attacks those who worship anyone besides God (e.g. angels or prophets) because those can neither create, nor give life, nor cause anyone to die. Yet, the Qur'an explicitly states that one angel or several angels are causing certain people to die [Sura 4:97, 16:28, 32, 32:11].
Confusion Concerning Identity of the Spirit and Gabriel (a long discussion of dozens of references)
'Iddah rules for divorced and widowed women appear to be arbitrary and inconsistent.
Is there a minimum age of marriage for girls?
To Marry or Not to Marry? The Qur'an forbids believers to marry idolatrous women [Sura 2:221], and calls Christians idolaters and unbelievers [9:28-33], but still allows Muslims to marry Christian women [5:5].
Will it be accepted of them or not?
Will Allah reward the good deeds of Unbelievers? S. 9:17 and 9:69 clearly say no. However, S. 99:7 implies yes. Moreover, S. 2:62 promises Christians reward for their good deeds. But S. 9:28-33; 5:17, 72-73 calls Christians idolaters, and S. 9:17 is very clear that idolaters will have no reward.
Should Muslims Accept Peace or Not?
Fighting All People Until They Do What?
Can They Disbelieve in the Last Day and be Safe?
Should Muslims show kindness to their parents? On the one hand, the Quran commands all Muslims to show kindness to their parents, even if they are disbelievers [17:23-24, 31:14-15, 29:8, etc.]. On the other hand, it demands not to show any love or friendship to those who oppose Muhammad, even if they are their parents [9:23, 58:22].
Can one be a believer in God and oppose Muhammad at the same time?
How many mothers does a Muslim have? Only one [58:2, the woman who gave birth and none else], or two [4:23, including the mother who nursed him], or at least ten [33:6]?