The second identifiable person to have his genome sequenced- James Watson- had around 30 known genome defects at the time. However most of them did not manifest as disease. That is a mystery.
No, it's only a mystery for people who have a truly simplified version of genetics and its relationship to disease phenotypes.
SNP changes in genes are not usually mutations that cause "defects". Most usually they increase or decrease risk for a disorder based on more of a polygenic profile.
For small enough values of defect, it is par for the course.