S.,
I have two kids and both have the same problem. I also felt incredibly guilty and still become anxious when we skip a brushing.
My daughter was 18 months when we discovered hers--the pediatrician told me many times that the marks on her teeth were nothing to worry about, but a friend thought it looked like decay. I brought her to a pediatric dentist in St. Paul who was awful. He told me I "did this" because he said I gave her a bottle before bed. She had never had a bottle in her life, she was exclusively breast-fed. Of course we found a new dentist who is supportive and wonderful, and we still go to him five years later. (Dave Elgethun at Dentistry for Children and Adolescents). She needed one cap and three fillings (her four front teeth). She had to have surgery to do the work, which was heartbreaking to me!
As soon as my second child's teeth erupted I took him in regularly. Despite the visits and my vigilance, he also developed tooth decay. We eat a whole grain diet, no soda, juice on special occasions only. He's almost four now and has had two teeth erode significantly--but the dentist says the decay is stopped now so we are going to leave his teeth as they are until they fall out. I just hope he doesn't get teased about them.
For both of my kids there were just a few teeth that had poor enamel, which was a relief.
I have met several families who have had similar experiences. I can't explain it!
Try to let yourself off the hook. Clearly you were doing the right thing by regularly brushing, and most dentists say to come in for a first visit at 3 years. Hopefully your baby won't have the same problem!