My 3+ weeks Baby had boils on inner thighs near genital area and also on scrotum. Siloderm Cream cleared boils leaving broken skin. Was it safe?

No harm. I don't think you did any harm but it sounds like your baby had/has a staph infection. There are no antibiotics in siloderm. I think if you are seeing open lesions, he should be checked and receive antibiotics. All the best.