Read this article at its new location here: https://reformedwiki.com/does-god-asking-adam-where-are-you-contradict-his-omniscience
God simply asked a question that He already knew the answer to. This is often done to teach something. So, God asking adam, "Where are you," does not mean that God is not omniscient.
Some argue that Genesis 3:9
It is common to ask questions that we know the answer to, which is exactly what God is doing in Genesis 3:9
God wanted to teach Adam something by asking the question, "Where are you?" The context of Genesis 3:9
So, the purpose of God's question to Adam probably also had a spiritual aspect to it. Perhaps the intent of God's question to Adam was something like this:
"Why are you hiding from me? Are you still in fellowship with me, or are you in rebellion against me?"
There is clearly no contradiction between Genesis 3:9
Some people have trouble accepting possible explanations to alleged contradictions in the Bible, especially ones that they consider a stretch. For example, Dan Barker, president of the Freedom From Religion Foundation, says this:
I have received numerous replies from Christians who think that these contradictions are either trivial or easily explained. Yet not a single "explanation" has been convincing.
The fact is that there are plausible explanations for every alleged contradiction in the Bible. That there is a plausible explanation for an alleged contradiction does not mean that it is definitely the correct explanation for the alleged contradiction.
However, as long as a possible explanation has been suggested, then it has been objectively demonstrated that there is no necessary contradiction regarding the Bible verses and passages brought up.
When people like Dan Barker say that they don't find a particular explanation for a contradiction "convincing," then that is merely their opinion. A plausible explanation has been suggested that eliminates the necessary alleged contradiction. They simply don't like it, which is not at all a relevant argument against the explanation.
To read more about solutions to Bible contradictions and difficulties, check out Norman Geisler's The Big Book of Bible Difficulties: Clear and Concise Answers from Genesis to Revelation. While we do not agree with some of Geisler's theology, particularly concerning his view of predestination, this book is still an excellent resource. It is thorough and filled with research.
Another book to check out is Tim Chaffey's Demolishing Supposed Bible Contradictions: Exploring Forty Alleged Contraditions, which also answers many alleged contradictions in the Bible.