The vaccine provides protection against the most popular strains but not all strains. People can get HPV from kissing or oral sex or from rubbing of genitals, etc. Did you do any of this before you two met? Did he? At this point, confrontation is not recommended because you are expecting his baby. He should assume that he has it too now. Playing detective on who gave it to who is not possible anyway. Since men cannot be blood tested, his "negative test results" obviously did not include HPV results. No man can ever tell if he is clean by any test.