I am looking for medically viable reasons why we might discover it to be more difficult than expected to bring pregnancies to term in space. This is for a society based approximately 75 years in the future that was forced into long-term space travel with limited time for preparation, which is to say technology is advanced but not perfected.
Radiation is the obvious answer, as L.Dutch pointed out. A fetus is particularly susceptible to radiation impacts as it is grown lots of new cells. An adult in space already has a lot of functioning cells of all the kinds he or she needs; but if a growing fetus can't generate these cells, it won't turn into a viable adult.
If for some reason, your spacecraft is kept at a lower than normal atmospheric pressure this might impact the ability to have children. Low barometric pressure can cause spontaneous labor, especially in women who are not acclimated to this lower pressure.
Possible reasons for keeping the craft at a lower pressure include the lack of enough atmosphere to go around. If you are forced to go into space suddenly, you might not have thought to bring your nitrogen bottles with you. If you build new space habitats or starships in space, you won't just be able to find some nitrogen lying around. If you have a limited supply, you might compromise on air pressure in your spacecraft.
Alternately, if you have a low amount of available gasses, you might keep various parts of the station at different pressures. For example, crops could be grown in a habitat module with lower air pressure and higher CO$_2$ pressure.
There are no studies of the effects of low gravity on pregnancy since there haven't been a lot. It would be easy to imagine a whole host of reasons that gravity could affect pregnancy. Extended time at zero-g can cause the heart to weaken, lowering blood pressure. Lowered blood pressure can cause miscarriages.
A fetus is a cradle of cellular multiplication. When a cell is splitting in two, its DNA is unfolded and more prone to damages by external agents.
Space environment is a soup of radiation, and you are putting the fetus in such a soup. A small damage to the DNA and the fetus cannot continue growing and thus survive.
I don't know why it is important for your story. So I also told you some stuff that I wouldn't consider a medically viable reason. But they could make the problem worse, even if you don't like them as sole reason.
If you go with radiation, because the space ships aren't shielded enough. hte egg cells in a fetus gets killed. Of course I would also expect some babies do have mutations and more people die because of cancer, if the radiation is not shielded enough.
We think you could give birth in space, because humans can give birth in water. But that is only a guess at the moment. It could be, that the head of the baby doesn't align itself. Or the umbilical cord goes around the head, because somehow inertia. They could have all c-sections, but operations in space are hard, because of the fluids you would need/want a special suit or room. So no fluids can go into equipment. For the same reason you would want special rooms, or suits for the baby making. (But I think it would not stop them from the baby making.)
Just not enough food. Lets say you only have 1 ton of carbon atoms on board. You could only make so much humans out of it. (10 ton of humans, with the assumption 10% of our mass is carbon atoms.) And you would need also carbon atoms for food. Even if you recycle every carbon atom. At a point you have no carbon atoms outside of humans. Not enough space... okay that is weak, especially if you want a generation ship. Were you replace only dead people. Politicians were stupid and split men and women on different ships... Yeah.. Really stupid.
Some material release some toxin into the air/food. And they can't get it out or find it or stop it, because without the material or machine all would die. So yeah, less babies get born.
**Social? aka stupid reasons **
It could be a society who doesn't like babies. Maybe because their religion says you can only have souls if you were born on earth. Or nobody wants to sex their children. So depending on population size in one ship, you could have an all male population. (Look below for a possibility) Or the opposite, everyone wants a boy. Or the 2nd generation doesn't like to be only considered breeders. Or only few are allowed to have children, so nobody wants any, because of envy from everybody else.
Through unlucky events, they get a population with less females. Maybe they started with 50 woman and 50 man because an evacuation wants to get everyone off planet. Not like a Generation ship which could send out an all female crew with frozen sperm that is selected for x chromosomes. And some freak accident happened and because of that 30 woman die or are now infertile.
Maybe they kept only few men for reproduction (Like they only let 1 in 100 male fertilized eggs develop into a child). Because men have then more children (~1000) than women (~8), you get more offspring, if you produce more sons (Even if the sons have only 1 in 100 chance of surviving). Since the sperm cells decide which sex the baby will have, the genes to produce more male offspring will get passed down easier. (From father to son, which produces more sons.) Lets say they let a lottery decide which male embryos get implanted into a willing mother. Then the genes that produces 800 males from 1000 fertilization have better chances to get picked up than genes that produces 500 from 1000. Worse when they find out what happened, most males only produce male offspring and only very rarely female. And nearly all females have the same genes for male only sperm. Meaning if one male gets a female offspring, that female will have still the same gene for more male offspring, which she would pass on to potential sons. Of course there could be other reasons making each issue worse.
Maybe have the same effect (lack of babies/miscarriage) with another explanation/reason, where you don't need to make assumption about medicine. When people really get pregnant in space, your book/world wouldn't need to be adjusted. I wouldn't believe a world exactly like our earth, except where plains can't fly because of different physics. I would believe that it is to expensive, because we don't have much aluminum and kerosene.
Some ideas I got from there: https://www.livescience.com/33047-space-sex-pregnancy.html