In the Name of Allah, Most Gracious, Most Merciful
I pray this message finds you well.
When reading the Qur'an, it's important to keep several points in mind:
1. The Qur'an is not a book of history, but rather a book of divine guidance, inspiration, laws, rulings, and accounts of past communities. Allah Most High reveals to us only that which we need to know in order to achieve felicity in this life and salvation in the Hereafter.
2. The creation story mentioned in the Qur'an does not give us a detailed description of how humanity spread forth from Adam and Eve (peace be upon them). In fact, the Qur'an only refers to the general details of the creation of Adam and his mate and the creation of humankind from them both. What the Qur'an emphasizes is the common origin of humanity and the fact that we were all created from this essence and imbued with a desire to worship and recognize the One True Lord.
3. The Qur'an does refer to the "two sons" of Adam, whom exegetes refer to as Habil and Qabil, or Abel and Cain. However, the moral of the story is that Abel and Cain both made offerings to Allah Ta'ala and only Abel's was accepted. As we know, Cain slew Abel and Allah Ta'ala then instructed Cain to bury his brother. Although Cain felt remorse, we understand from this account that human beings are capable of two extremes. Cain went to the extreme of taking Abel's life, while Abel was God-fearing and refused to harm Cain.
4. The Qur'an does not tell us how the earth was populated by the progeny of Adam and Eve. However, this is not the point. The point is that Adam and Eve were both created as signs of Allah's wisdom and power and sent down to earth to act as Allah's vicegerents, or khalifa.
Now we do know from some commentaries that Adam and Eve had two sets of twins, each set including a boy and girl. We are told that the boy from the first set married the girl from the second set, while the girl from the first set married the boy from the second set.
We have to be cautious, however, about looking at this story in terms of incest. From what I have studied, this story has not been elaborated. The general principle is that the marriage of the sets of twins was an exception granted to the first generation of human beings.
Allah Most High says,
"To thee We sent the Scripture in truth, confirming the scripture that
came before it, and guarding it in safety: so judge between them by
what Allah hath revealed, and follow not their vain desires, diverging
from the Truth that hath come to thee. To each among you have we
prescribed a law and an open way. If Allah had so willed, He would have
made you a single people, but (His plan is) to test you in what He hath
given you: so strive as in a race in all virtues. The goal of you all
is to Allah. it is He that will show you the truth of the matters in
which ye dispute" (5:48).
We know that rulings may change according to people's changing circumstances. Previous prophets came with laws that were valid for their communities, but were then either confirmed or abrogated by later revelations. Prophet Muhammad, Allah bless him and give him peace, was sent as the Seal of Prophethood with the final revelation that superseded all previous laws.
In conclusion, it's best not to worry about the details of matters that do not benefit one in either their religion or worldly life. We read the Qur'an as a book of divine guidance, not as an historical narrative.
And Allah knows best.