Here are some possible scenarios, although they sound crazy:
1. Your husband had sex before he met you, got infected with the virus and didn't show symptoms due to a strong immune system and good health. No man is "cleared" of this virus until they come up with a reliable test for HPV in men. He could not have been tested for this virus. Most people who become infected with genital HPV will not have any symptoms and will not know they have an infection. It has been estimated that fewer than 5% of people with genital HPV will develop warts. The others have subclinical (or invisible) HPV. Whether people with subclinical HPV infection are as contagious as people who have visible warts is not known.
2. You had sex before you met your husband, got infected with the virus but had a strong enough immune system to keep it dormant until now. Pregancy does lower a woman's immune system. That a wart did not appear during your first pregnancy was due to a stronger immune system then when you were younger and probably healthier.
3. The doctor is in error and you need a second opinion. Which I hope it is.
There are cases where 10-20 years go by and monogamous people suddenly get a wart because they were not virgins when they met. This is usually due to no sleep/stress/bad colds when people are the most vulnerable. If it is a wart, you should get it removed and biopsied to determine the strain.
Good luck!