We can say with some degree of certainty that certain behaviors by the mother increase the chances of having below average birth weights or of causing birth defects, for example. But an increased chance does not guarantee low birth weight or birth defects. An increased chance is not a direct cause. Even if these do occur, there is no way to determine with any degree of certainty, that the behavior of the mother is the direct cause or even the primary cause. An as yet not understood combination of factors might create the same results and those results may not affect every pregnant woman or affect every one in the same way.
Different people react differently to the same things.
For some people, taking penicillin can cause death. For others, it can prevent it. There are too many variables involved, especially when dealing with prenatal medicine. We're still not sure what can and what cannot cross the placental barrier. Or what effect the mother's state of mind has on a baby.