At the beginning, when Jane and Maura are in the clay baths, in close shots there is a large smear on Jane's face. In far shots there is nothing on her face.
Just because the mother is Type A and her offspring is Type O doesn't automatically eliminate the mother as the biological mother. The mother can still carry the recessive O allele that can show up on her offspring if the father at least one O allele.
Dr. Isles mentions that the baby is O+. But since the woman is A it cannot be this woman's baby. This is false. The mother could be heterozygous for A type blood. The father could be heterozygous for A or B. Or the father could also be O. Positive and negative are unrelated to this (kind of). The woman would need to also be + to prevent Rh incompatibility.