What makes oral contraceptives only 97%-99% effective and not 100%?

Life is not perfect: Life is never perfect nor 100%. Things just happen, sometimes. Each woman's body has to respond to the artificial hormones in the pills, and maybe once in a rare while she still manages to ovulate. The percentages are about a population of women, NOT about one woman. Medical statistics have to be interpreted this way, because nobody knows what the percentage effectiveness is for a specific woman.

Human Factors: The most common reason for oral contraception failure is incorrect use (Missing pills, starting wrong, etc). Other common causes are antibiotics, vomiting up the pills, etc. The chance of pregnancy during the first year if the pill is taken perfectly is low, 0.3%. "Perfect use" pregnancies are probably due to failure to suppress ovulation. Best Wishes!