I think the breastfeeding debate is a great example. The studies showing any non-trivial advantages are tenuous, and often fail to detect any statistically significant advantage at all. At the same time, doctors completely and thoroughly fail to analyze these decisions in a rational cost/benefit way. Breastfeeding is a tremendous burden on career women. If not breastfeeding enables a woman to get back to work sooner, get less behind on her career progression, etc, then there is a monetary benefit to not breastfeeding, a very concrete one one that must be balanced against the tenuous and uncertain costs of not breastfeeding.
Same thing for drinking during pregnancy: http://www.huffingtonpost.com/peggy-drexler/-a-loaded-questi.... I recommend reading the Peggy Drexler article, it's wonderful.
Same thing for caffeine: http://www.webmd.com/baby/news/20100721/moderate-coffee-drin.... Note that: 1) 200 mg is about two and a half red-bulls, and 2) exercising, something which doctors recommend to pregnant women without reservation, has been linked to similar increases in risk of miscarriage as heavy caffeine consumption.
When it comes to pregnant women, the medical communities recommendations are wildly unscientific and highly irrational.
What unjustified advice did your wife get?