All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
Before answering your question, we would like to draw your attention to the fact that the verse which you referred to (in the question) is not about the usual way of the creation of man. Rather, it is something that Allaah The Almighty wished to show to ‘Uzayr (Ezra) when he found it strange as to how life would come back to a town by which he passed through and which he found that it had tumbled over its roots.
As for your question, we do not know how you found that this (making bones first and then clothing them with flesh) contradicts modern science. What we know from what some specialists in the field of embryology (studying the stages of the creation of man) say that the bones are formed (in the fetus) prior to the formation of the flesh on them, and that this does not happen at the same time, and this is in conformity to the texts of revelation.
Finally, it should be noted that a clear text from the Quran or the Sunnah can never contradict sound reason; we clarified this in Fatwa 92208.
Allaah Knows best.