Readers may consult the complete verses in Online Quran.

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A note to the readers

In Part 1, I wrote that verses 2:51 and 7:142 contradicted. However, the Qur’an says in both the verses that Moses' appointment with Allah was for forty nights. Verse 2:51 clearly says forty nights. Yusuf Ali translates 7:142 in this manner (to be fair, please ignore Yusuf Ali’s insertions inside the parentheses):

We appointed for Moses thirty nights, and completed (the period) with ten (more): thus was completed the term (of communion) with his Lord, forty nights. And Moses had charged his brother Aaron (before he went up): "Act for me amongst my people: Do right, and follow not the way of those who do mischief."

Ibn Kathir explains the ambiguity in this manner:

‘Allah reminds the Children of Israel of the guidance that He sent to them by speaking directly to Musa and revealing the Tawrah to him. In it, was their law and the details of their legislation. Allah stated here that He appointed thirty nights for Musa. The scholars of Tafsir said that Musa fasted this period, and when they ended, Musa cleaned his teeth with a twig. Allah commanded him to complete the term adding ten more days, making the total forty. When the appointed term finished, Musa was about to return to Mount Tur.’

This explanation is confusing. To say the least—could it that Allah’s instruction to Moses was to fast during night (forty nights in total) and seek audience with Allah during the day (forty days in total). It could be either. I chose the first option: that is, Moses fasted during nights and met Allah during day.

Nevertheless, it appears that ibn Kathir might be incorrect if we are to accept the original Arabic version of this verse.

I apologize to the readers for creating misunderstanding because of ibn Kathir’s tafsir.

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Sura 3: al-Imran (The Family of Imran)

3:2
Worship none but Allah; He is the ever-living, and the sustainer of all things.
Contradiction: 12:100 says Allah allowed Joseph’s brethren and his parents to worship Joseph.

3:3
Allah sent the Qur’an to Muhammad (the ENTIRE Qur’an).
Contradiction: 17:106, 25:32 say Allah sent the Qur’an in stages.

3:7
Allah has sent down the Book. Only men of understanding will grasp the messages of the Qur’an; some verses are basic some are allegorical; perverse hearts follow allegorical verses to find hidden meanings to make discord; only Allah knows the hidden meanings of the Qur’an.
Contradiction: 16:103 says the Qur'an is in clear Arabic.

3:18
Allah, His angels, and the knowledgeable people bear witness that none is to be worshipped except Him. Maintaining His creation is justice.
Contradiction: 12:100 says Allah allowed Joseph’s brethren and his parents to prostrate before (worship) Joseph.

3:20
Muhammad's duty is only to convey the messages of Allah. (Allah has sent Muhammad to the illiterate Arabs—ibn Kathir)
Contradiction: Allah says in 8:39 if the unbelievers do not convert to Islam fight them.

3:33-34
Allah chose the families of Adam, Noah, Abraham, and Imran above all people.
Contradiction: 2:47, 45:16-17 say Allah favored the Children of Israel above all beings.
Contradiction: 3:42 says Allah preferred Mary above all women.

3:41: The angel (Gabriel) instructed Zachariya to remain silent for three days, communicating only through signs, and offering two prayers—in the evening and in the morning.
Contradiction: in 19:10 Allah commanded Zachariya to remain silent for three nights.

3:42
Angels told Mary that she is chosen above women of nations.
Contradiction: 19:17 says one angel, as a man, spoke to Mary.
Contradiction: 2:47, 45:16-17 say Allah preferred the children of Israel above all beings.

3:45
The angels told Maryam (Mary) that she would give birth to Jesus, a Word (manifestation) of Allah and Jesus will be held in great honor, and he will be nearest to Allah.
Contradiction: 19:17 says an angel, in the shape of a man, visited Mary.
Contradiction: in 21:98 Allah says all objects worshipped by men besides Allah will be in hell, i.e., Jesus will burn in hell.

3:59
Allah created Adam from dust, Allah said ‘be’ and Adam was there; Jesus looked like Adam (as Allah made Jesus without a father He made him look like Adam, and because Adam had no father or mother, Allah created Adam from dust—ibn Kathir).
Contradiction: 38:71 says Allah created Adam out of wet clay..
Contradiction: 15:26 says Allah created Adam out of sounding (black burnt) clay and mud.
Contradiction: 38:75 says Allah created Adam with His two hands.

3:67
Abraham was not a Jew, nor a Christian, but a Muslim (Hanif), and Muhammad is the nearest to Abraham.
Contradiction: Allah says in 6:14 that Muhammad was the first Muslim.
Contradiction: 7:143 says Moses was the first to believe in Islam.
Contradiction: 2:37 says Adam was the first Muslim.
Contradiction: 26:51 says some Egyptians were the first Muslims.

3:78
Some Jews and Christians twisted Allah’s scriptures and passed them as Allah’s messages.
Contradiction: 6:34, 6:115 say none can alter the words of Allah.

3:85
Allah will not accept any religion other than Islam.
Contradiction: 2:62 says Allah will reward Christians, Jews and the Sabians.

3:97
Mecca is the station of Abraham: if you can afford then perform pilgrimage (hajj) in Mecca; Allah does not need ‘Alamin’(any of His creatures).
Contradiction: in 2:21 Allah says He needs mankind to worship Him.
Contradiction: 51:56 says Allah needs humans and jinns to worship Him.

3:125
In Badr, Allah made a terrific onslaught with five thousand angels. (The angels wore white wool and had special markings distinguishing their horses—ibn Kathir)
Contradiction: 8:9 says in Badr, Allah helped the Muslims with one thousand angels.

3:144
Muhammad is no more than an apostle; apostles before him had died.
Contradiction: 4:157 says Allah raised Jesus up; Jesus did not die.

3:169-171
Those slain in Allah’s way (in Jihad) do not die; they live in the presence of Allah (in Islamic Paradise), and enjoy His provisions.
Contradiction: 19:70-71 say every soul, including that of a Muslim, at least for some time, will be in hell.

3:180
Allah does not like stingy people; Allah will tie the covetous articles like twisted collars in the necks of unbelievers. Allah is the inheritor of the heavens and the earth.
Contradiction: 2:116, 3:189, 20:6, 21:19, 57:2 say Allah is the owner of all things in the heavens and in earth.

3:189
Sovereignty of the heavens and the earth belongs to Allah.
Contradiction: Allah says in 3:180, 15:23, 19:40, 19:80, 21:89, 28:58 He inherits from other infidels and other creatures.

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Sura 4: an-Nisa (Women)
 

4:5
Take care of the minor orphans’ property and do not handover their property to them while they remain minor (until they are marriageable).
Contradiction: 65:4-5 says prepubescent girls (minor girls) can be married.

4:6
Test the orphans for their maturity; release properties to orphans when they are capable of sound judgment (i.e., have attained maturity or puberty, usually taken as fifteen years of age. It is the marriageable age—Jalalyn. The age of puberty is the marriageable age—ibn Abbas).
Contradiction: 65:4-5 says prepubescent girls can be married.

4:15
If a woman is lewd confine her in house till death (basis of honor killing in Islam); four believing male witnesses are required to prove a woman’s innocence.
Contradiction: in 24:2 Allah prescribes one hundred lashes for both men and women who perform lewdness.

4:16
Allah prescribes unspecified punishment for lewdness by men; (homosexuality, gays—ibn Kathir); if the perpetrators repent then leave them alone.
Contradiction: in 24:2 Allah prescribes one hundred lashes for both men and women who do acts of homosexuality.
Contradiction: 4:15 says permanent house arrest, until they die, for women.

4:18
Inflict the most grievous punishment for dying rejecting faith (i.e., those apostates who die as apostates.)
Contradiction: 10:90 says Pharaoh submitted to Islam when flood engulfed him.

4:46
Majority of the Jews distort the meaning of words by a twist of their tongues; Allah condemns them.
Contradiction: 6:34, 6:115 say none can alter the words of Allah.

4:48
Allah forgives every sin except idolatry (shrik).
Contradiction: in 4:153 Allah forgave the idolatry of Moses’ people.

4:75
Fight against oppression; Allah raises a protector from among the believers.
Contradiction: 9:116, 17:111, 32:4 and 42:28 say Allah is the only protector and helper.
Contradiction: 41:31, 32 say angels are our protectors in this life and the life hereafter.
Contradiction: 5:55 says Allah’s messengers are our protectors.

4:78
Death will find you even if you are in towers built up strong and high. All things are from Allah.
Contradiction: in 4:120, 38:41 Allah says evil things are from Satan.
Contradiction: 4:79 says evil things are from us.

4:79
Good things are from Allah; evil things are from one’s own soul. Allah is the witness that Muhammad had been sent as a Messenger to people.
Contradiction: 4:120 and 38:41 say evil things are from Satan.
Contradiction: 4:78 says all things; including evil things, are from Allah.

4:93
A dreadful penalty (hell, unspecified) is for a Muslim for intentionally killing another Muslim.
Contradiction: 2:178 says whoever kills deliberately must be killed, or if he is pardoned he must pay the blood money.

4:107
Allah does not like disloyalty.
Contradiction: 63:5 says Allah might forgive the hypocrites if Muhammad sought Allah’s forgiveness for them.

4:116
Except the idolaters (shrik), Allah forgives whomever He pleases.
Contradiction: 4:153 says Allah forgave the calf-worshippers of Moses’ people.

4:120
Satan creates false desires; Satan deceives people.
Contradiction: 16:93 says Allah misleads who He wishes.
Contradiction: 4:78 says all things are from Allah.

4:150-151
Allah will severely punish those who deny Allah and Muhammad and those who separate Allah from His messengers.
Contradiction: 2:62 says Muslims/Jews/Christians/Sabians—anyone who believes in Allah and the last Day and does a righteous deed will get rewards.

4:152
The believers should not make distinctions among the messengers; in the hereafter; Allah will reward such believers.
Contradiction: 2:253, 17:55 say Allah preferred some prophets over others.

4:153
For asking Moses to show them Allah in public, Allah dazed people with thunder and lightning. Allah forgave Moses people who worshipped the golden calf.
Contradiction: 4:48 says Allah does not forgive idolatry, that is, shrik.
Contradiction: 2:63 says Allah terrorized Moses’ people by raising the Mount Sinai above them.

4:157
Jesus was not crucified; he did not die.
Contradiction: 3:144 says all prophets before Muhammad had died.
Contradiction: 23:15, 39:30 say everyone will die.

4:158
Allah raised Jesus up alive.
Contradiction: 21:98 says all objects worshipped by men besides Allah will be in Islamic hell; i.e., Jesus will burn in hell because the Christians worship him.

4:171
People of the Book are not to commit excesses in their religion; Jesus was only another apostle of Allah, he was the Word (manifestation) of Allah; Jesus is also a spirit from Allah; so, no Trinity.
Contradiction: 4:172 says Allah made Jesus His servant.

4:172
Christ (Messiah, Jesus) was a servant of Allah.
Contradiction: 4:171 says Jesus is a spirit and Word of Allah.

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Part 1 | Part 2 | Part 3 | Part 4 | Part 5 | Part 6 | Part 7 | Part 8 | Part 9 | Part 10.