A number of contradictions have been alleged against the Qur’an. We shall analyze these contradictions and see if they are of any worth or are merely attempts at arriving at some sort of contradiction.
The original anti-Islamic claim puts up four alleged contradictions but repeats the first one in the end where it is briefed in the beginning and detailed in the end and hence puts forth only three alleged contradictions in reality.
Alleged contradiction 1
It is asked whether Allah misguides only the disbelievers (Qur’an 2:26) or does he also misguide the believers (Qur’an 4:157-159)! This is a clear case of misreading. Qur’an 4:157-159 do not speak of misguiding the believers at all; they speak of the misguidance of those who boasted of killing Prophet Eisa (Jesus) (عليه السلام). The attempted killers of a messenger of God cannot be believers of that same messenger and this is a contradiction on its own. However, if it is argued that the believers also were deceived into thinking that Prophet Eisa (عليه السلام) was crucified. This view is arrived at if one ignores history and decides to form an opinion based on selective pick and choose reading. The banned books of the Bible confirm that what had really happened with Prophet Eisa (عليه السلام) was made clear during that time itself. The gospel of Barnabas also testifies to this. Even if we ignore the banned books and base the New Testament as our source of history, we reach the same conclusion. Besides, The New Testament proves that during the same time, there were people (in large numbers) who did not believe in crucifixion who are being rebuked by Paul  in Galatians 3:1 for denying crucifixion.
Alleged contradiction 2
It is stated that the Qur’an mentions that Allah strengthens and keeps firm the believers (Qur’an 14:27) and hence as per this statement there should be no apostates since if there are apostates, then they were not kept firm by Allah when they were Muslims. It is said that Qur’an 4:88 contradicts Qur’an 14:27 as 4:88 states that some believers had been led astray.
This is another case of misreading. Qur’an 4:88 speaks of the hypocrites and they were never believers in the first place. Faith had not entered their hearts even though they admitted to be believers by their tongues. An enemy of Islam pretending to be a Muslim with the aim to destroy Islam from within would not be considered a believer in the first place and hence such ‘believers’ being led astray would not contradict the statement of Allah in Qur’an 14:27 which reads as follows:
يُثَبِّتُ اللَّهُ الَّذِينَ ءَامَنُواْ بِالْقَوْلِ الثَّابِتِ فِى الْحَيَوةِ الدُّنْيَا وَفِى الاٌّخِرَةِ وَيُضِلُّ اللَّهُ الظَّـلِمِينَ وَيَفْعَلُ اللَّهُ مَا يَشَآءُ
Allah keeps firm those who believe, with the firm word, in worldly life and in the Hereafter. And Allah sends astray the wrongdoers. And Allah does what He wills.
Pondering over the emphasized parts would lead one to the same conclusion stated above. Ibn Kathir explains the verse as follows:
When the Muslim is questioned in the grave, he will testify that, `La ilaha illallah’, and that Muhammad is Allah’s Messenger, hence Allah’s statement, (Allah will keep firm those who believe, with word that stands firm in this world, and in the Hereafter.) Muslim and the rest of the Group recorded it. Imam Ahmad recorded that Al-Bara bin `Azib said, “We went with the Messenger of Allah to attend a funeral procession of an Ansari man. We reached the grave site when it had not yet been completed. The Messenger of Allah sat, and we sat all around him, as if there were birds hovering above our heads. The Prophet was holding a piece of wood in his hand, poking the ground with it.
Read more here.
Alleged contradiction 3
Quoting Qur’an 31:30 and 2:26, it is asked whether Allah is the truth or does he misguide the disbelievers! The alleger lays down the following points from these two verses:
1) If Allah is the truth, He cannot misguide
2) Allah is the truth
3) Therefore He cannot misguide
While explaining these points, the alleger puts forth further points he has derived:
1) If Allah is infinitely Merciful and Gracious then Allah would give the disbelievers the ability to repent and an unlimited amount of opportunities to repent
2) Allah is infinitely Merciful and Gracious
3) Therefore Allah would give the disbelievers the ability and chance to repent an unlimited amount of times.
This confusion on the part of the alleger is not a surprise. Without going in detail in understanding the meaning behind the verses, one is bound to make such mistakes and the arising of such doubts and questions would result naturally. However, once the purpose of this misguiding the disbelievers is explained, the doubts should remain no more.
We know from the Qur’an that life is a test for the Hereafter. At the time of death, this test is over and therefore, a person has the chances of increasing in good or bad till then. The Qur’an mentions that for some people heaven and hell are decided upon the earth within their life.
The Qur’an mentions that for some people, Allah has decreed paradise while they are still alive.
إِنَّ الَّذِينَ سَبَقَتْ لَهُمْ مِّنَّا الْحُسْنَى أُوْلَـئِكَ عَنْهَا مُبْعَدُونَ
But those, for whom the decree of joy and happiness had been issued by Us, will be spared the above fate!
The Hadith of the ten blessed companions is a further support to this claim.
Likewise, the same is for hell.
وَكَثِيرٌ حَقَّ عَلَيْهِ الْعَذَابُ
…but upon many the punishment has been justified…
Perhaps the biggest example of this would be Abu Lahab (Surah 111) who had been doomed to hell while he was still alive.
A saying of Imam Ahmad Ibn Hanbal speaks along the same lines:
Whoever speaks ill of the (righteous) scholars, Allah will give death to that person’s heart before He will give death to that person.
Hafiz Ibn ‘Asakir said:
It is known that Allah causes the heart (of the one who does this) to die before their body dies.
Life is a test for the Hereafter and since Allah is the giver of life and death and one find no issues with the test ending upon the person’s death, why does one find issues with the test ending within the person’s lifetime? The criterion for the test to end is normally death which is caused by Allah. Hence we know that the criteria, timings etc. for the start the start of the test are with Allah and therefore, if Allah chooses to end the test for someone before his death should not be questioned. This would be dealing in double standards since originally the concept of the end of test through death has not been challenged.
One may ask as to why these people are kept alive if hell is already decided for them! The answer is that such people are kept alive for the test of other people for whom the test has not ended. Abu Lahab, an enemy of the Prophet (ﷺ) was given the penalty of hell within his lifetime which meant that he had been given sufficient time and chances by Allah and Allah had decided to end his test but did not give him death immediately for the tests of others around him. Allah could have made the entire humanity as one nation standing upon the truth but then the whole purpose of this life being a test would not have been fulfilled and mankind would have been like angels without free will. For the proper test, free will is required which is what Allah has given to mankind.
Indeed, Allah knows the best.
 Sunan Abu Dawood, 40:4632 and Tirmidhi, Hadith 3747