See below from the Mayo clinic. I'm a vegetarian who eats soy pretty regularly, and my midwife doesn't seem concerned, as I try to eat it in moderation.
From
http://www.mayoclinic.com/health/soy/NS_patient-soy/DSECTION=safety
Pregnancy and Breastfeeding
Soy as a part of the regular diet is traditionally considered to be safe during pregnancy and breastfeeding, although scientific research is limited in these areas. The effects of high doses of soy or soy isoflavones in humans are not clear, and therefore are not recommended.
Recent study demonstrates that isoflavones, which may have estrogen-like properties, are transferred through breast milk from mothers to infants. High doses of isoflavones given to pregnant animals have resulted in tumors and reproductive changes in offspring, although this has not been tested in humans.
In one human study, male infants born to women who ingested soymilk or soy products during pregnancy experienced more frequent hypospadias (a birth defect in which the urethral meatus, the opening from which urine passes, is abnormally positioned on the underside of the penis). However, other human and animal studies have examined males or females fed soy formula as infants, and have not found abnormalities in infant growth, head circumference, height, weight, occurrence of puberty, menstruation, or reproductive ability.
Research in children during the first year of life has found that the substitution of soy formula for cow's milk may be associated with significantly lower bone mineral density. Parents considering the use of soy formula should speak with qualified healthcare practitioners to make sure the appropriate vitamins and minerals are provided in the formula.