Personally, I think Muhammad is referring to the concept of Incarnation and the co-mingling of body and spirit.
They say, " Allah has taken a son." Exalted is He! Rather, to Him belongs whatever is in the heavens and the earth. All are devoutly obedient to Him, 2:116
Never has God begotten a son, nor is there any other god besides Him. Were this otherwise, each god would govern his own creation, each holding himself above the other. Exalted be God above their falsehoods! 23:91
[He is] Originator of the heavens and the earth. How could He have a son when He does not have a companion and He created all things? And He is, of all things, Knowing. 6:101
Those who say: ‘The Lord of Mercy has begotten a son,’ preach a monstrous falsehood, at which the very heavens might crack, the earth break asunder, and the mountains crumble to dust. That they should ascribe a son to the Merciful, when it does not become the Lord of Mercy to beget one! 19:88
He (exalted be the glory of our Lord!) has taken no wife, nor has He begotten any children. The Blaspheming One among us has uttered a wanton falsehood against God, although we had supposed no man or jinee could tell of Him what is untrue.72:3
The question must be asked, who is teh author of the quran referring to here? The author of the quran seems to have in mind that for God to have a son, he needs a consort, then goes on to brand this as ludicrous because God has no consort. The only thing is, no one believes (at least among jews and Christians) that God had a consort in order to have begotten a son. Is the author of the quran speaking to Christians who definetely seem to be in mind in verses where it mentions Jesus and him being called a son.
So if the quran is refferring to the incarnation, and condemning the viewpoint that Jesus is the begotten son of God because he was incarnate and born of a virgin, you have a problem. Christians didn’t believe this, they believed Jesus was begotten of the father before time was. To recite the creed.
And in one Lord Jesus Christ, the only-begotten Son of God, begotten of the Father before all worlds (æons), Light of Light, very God of very God, begotten, not made, being of one substance with the Father; Nicene/Constantinopolitan creed. The idea of Christians, at least by the time of Muhammad is that Christ was always begotten by God before even creation itself. The son does what the father wills, the son is totally loyal to his father and the father is totally faithful to his son in all things.
So if your interpretation of the quran is correct, the quran is wrong. I think it is just as wrong on the muslim interpretation which I think accurately reflects the quran.