There are numerous stages in fetal development where certain types of differentiation occur. For instance, pregnant mothers who are alcoholics disrupt certain developmental states, leaving their fetuses with wide-set eyes, thin lips, and mild to moderate retardation. It's called fetal alcohol syndrome.
Other substances have been found to cause disruption at other stages. For instance, the drug thalidomide was found to cause problems in fetuses as their limbs were forming, which often led to absent or underdeveloped arms or legs.
In the case of sex differentiation, this occurs fairly late in fetal development. Until a certain point all fetuses are essentially female, until androgens cause male specific traits to appear in fetuses with XY chromosome pattern. If those androgens are not present or blocked for some reason, the phase of genital differentiation never occurs.
All sorts of interesting things can happen to the body and brain while a fetus is developing. Perhaps someday researchers will have some definitive answers on all the effects various levels of hormones can have on a developing fetus.
In the meantime, they know for sure that it's best for any woman who even thinks she might be pregnant to consult with a physician about any medications she may be taking.
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