The Natural man does not understand the Scriptures to be true

 "The natural man according to Paul does not understand the true significance of the words and deeds of his fellow-men; he does not use them to attest spiritual facts. The man who is in Christ, on the contrary, even when he uses ordinary means of information, is acquiring knowledge of spiritual relationships, relationships which exist in the new world. So it is also with the knowledge of Christ. The natural man may acquire a certain knowledge of Christ; he may learn what Christ said and did and what were the worldly circumstances of His life. But such knowledge is a knowledge according to the flesh; it does not attain to the true significance even of those facts which are learned." - J. Gresham Machen, The Origin of Paul's Religion, Page 56

It is not that one believes facts only and another does not believe facts only. The difference Machen is talking about is that one understands the facts and believes them in their true import, the other does not.