Fact 1: [112:1-4]: Say, "He is Allah, [who is] One, Allah, the Eternal Refuge. He (God) neither begets nor is born. Nor is there to Him any equivalent."
Fact 2: [2:117]: “Originator of the heavens and the earth. When He decrees a matter, He only says to it, "Be," and it is.”
Allah does not beget, but if Mary had a child without a husband then Allah made Jesus happen, Allah begot Jesus.
As Allah said 'be' He foresaw that Mary would marry and have Jesus. When He says 'be' He knows it will happen, it is not a miraculous event.
Both verses understood this way compliment, not contradict each other.
When Allah said 'be' and the universe came into existence, did every star, planet, animal, plant come into being in their completed form or did they undergo a process of development, 'creation, evolution? As Quran confirms development, then you you must likewise see the natural coming into existence of Jesus, not a fatherless one!
6:73 And He is the One Who has created the heavens and earth with a definite purpose. Whenever He says "Be!" it is. His Word is the truth. And His will be the Dominion on the Day the Trumpet (of Resurrection) is blown. Knower of the Invisible and the Visible, for, He is the Wise, the Aware. [3:191, 38:27]
21:30 Are the disbelievers not aware that the heavens and earth used to be one solid mass and We exploded them asunder? And that out of water We made every living thing? Will they not, then, acknowledge the truth? [Here is a clear allusion to the Big Bang theory. Numerous celestial bodies came into being and started swimming along in their orbits. Almost all modern astrophysicists believe that this Universe has originated as one entity from one single element, hydrogen that, in stages, became consolidated with gravity and then broke apart into celestial bodies. (Muhammad Asad). 21:33, 24:45, 36:40, 79:30]
41:11 Likewise, He is the One Who designed well the Sky when it was Smoke (Nebulae of gas). And He said to it and the earth, "Come both of you willingly or unwillingly." They said, "We do come, obedient." [Thumm = Afterward, then, so, likewise, similarly, in the like manner. The Cosmic bodies coming into their orbits willingly or unwillingly indicates their being inherently subservient to Divine laws, unlike humans who have been granted free will. 3:82, 13:15]