Quran verse 4:40 says “Indeed, Allah never wrongs anyone—even by an atom’s weight. And if it is a good deed, He will multiply it many times over and will give a great reward out of His grace.”

But in verse 34:3 he says “But those who disbelieve say, "The Hour will not come to us." Say, "Yes, by my Lord, it will surely come to you. [Allāh is] the Knower of the unseen." Not absent from Him is an atom’s weight within the heavens or within the earth or [what is] smaller than that or greater, except that it is in a clear register -“

Yhe key distinction in the first verse he says an atoms weight and the next he says an atoms weight and anything smaller or larger. As we know today atoms have smaller contents inside known as electrons and protons. How do you reconcile both these verses. A thought crossed my mind that in the first verse Allah(swt) could wrong someone by something smaller than an atoms weight. Astaghfurallah for saying it but that’s what I’m understanding from the first verse

No the first verse is not indicating that Allah will oppress but less than the size of the atom. At the time of revelation, Arabs considered the “dharra” to be the smallest thing or particle in existence. So the first verse is saying Allah won’t oppress anyone, even to this small extent.

As for the other verse, it’s saying nothing escapes the knowledge of Allah—even if something is smaller than a dharra He knows of it. So it’s just making it clear that He knows of the smallest things in existence.