It is my understanding that Crinone is one of two prog. supplements that are approved to take during ttc and early pregnancy.
http://www.ivf1.com/crinone/
Many, many women here use progesterone supplements up til the time the placenta takes over the production. Usually 12-14wks. I assume they rx'd the vaginal suppositories? That is usually the best way it is absorbed by the body. The above link explains a little. While there is no medical evidence that administering progesterone is beneficial, there is also nothing to disprove it.
As for the neural tube defect, were you tested for MTHFR gene? Some women do not circulate folate due to this condition. Most neural tube defects happen in the earliest weeks of pg due to a folic acid defiency. Many were taking their folic acid, not aware their bodies weren't using it. I am sorry for your loss and congratulations on the new baby!