There are a couple of Scriptures which allude to the answer. First, when God created Adam and Eve, He told them, "Be fruitful and multiply, and fill the earth." (Genesis 1:28) Again, He told Jacob to "be fruitful and multiply; A nation and a company of nations shall come from you, and kings shall come forth from you." (Genesis 35:11)
If God were creating each person separately, why would He give Adam and Eve, and Jacob, this responsibility to multiply?
We learn a little about how God works with humans from the way He created the animals. He used very similar words when He blessed the animals saying, "Be fruitful and multiply, and fill the waters in the seas, and let birds multiply on the earth." (Genesis 1:22) And, in Genesis 1:24, God said "Let the earth bring forth living creatures after their kind."
So, we see that God created the pair of animals and made them where they could bring forth after their kind. God did the same with humans. He specifically created Adam and Eve and gave them the ability to procreate, to fill the earth without His special intervention with each one.
One important thing to note: God allows humans to make mistakes and even to do wrong things when they procreate. One example is when the angels saw human women and chose to have children with them. Their offspring were not authorized by God, but were still created using the natural processes. Those offspring became very evil (Genesis 6:2-7). They became so evil that God destroyed them in the Flood. Only Noah was "perfect in his generations”, i.e. his lineage was traced back to Adam and was not defiled by the fallen angels. He and his family were saved from the flood and continued the human race.
God does not create ill, deformed babies. The physical, emotional, and spiritual deformities we have are a result of sin and were not created by God. (Deuteronomy 32:4, “…his work is perfect…” )
When God told Adam, “…of the tree of the knowledge of good and evil, thou shalt not eat of it: for in the day that thou latest thereof thou shalt surely die”, the margin translates the Hebrew as reading “dying thou shalt die.” (Genesis 2:17) We all inherit imperfection and are born dying.
Because God does not specifically create the fallen human being does not mean He does not know us. We know other people, but we did not create them. God knows everyone so well that each person will be resurrected with their unique attributes. Yes, even the hairs of our heads are numbered. (Luke 12:7)
However, God can indeed over-rule the birth of a person. God has and does specially chose individuals to play prominent roles in the outworking of His plan. Samson’s mother was to abstain from grapes from Samson’s conception (Judges 13:14), and we believe God knew Samson’s character from inception. Yet, that does not mean that God specially created a sinful, angry, disobedient Samson. God did foreknow how the genetic inheritance, the family nurturing, the influence of the society of Israel and the world were going to impact this baby. God also knew He could use Samson to free Israel.
When God planned the creation of the earth and the specific creation of Adam and Eve, He wanted the earth to be populated with perfect, obedient, wise, happy people. How God planned to achieve this wonderful outcome has been a mystery to mankind. The Bible teaches that God foresaw Adam’s fall into sin and that He had already designed a plan of redemption for our race “…redeemed with precious blood, as of a lamb unblemished and spotless…foreknown before the foundation of the world…” I Peter 1:18-20.
When Jesus redeems every single man, woman, and child in the resurrection, mankind will awaken having experienced the dreadful results of sin. Then Christ will heal all deformities of mind, body and spirit (Isaiah 35 especially verses 5 and 6) and the nations will be taught righteousness (Jeremiah 31:34). At the end of Christ’s 1,000 year reign, mankind’s obedience to God will again be tested. However, then people will know the results of sin versus the joyous fruits of obedience and most will rejoice to follow God’s will forever as perfect, wise, and happy people (Revelation 21:4).