In the latest patch? If so, that's interesting. In my last playthrough, was clan tier 2, no babies, literally 2 days after tier 3 she got pregnant and stayed pregnant for the next few years with brief breaks between lasting only a few days. Perhaps it was just luck, but it seemed pretty clear that as of 1.56, if you are not high enough tier to go to the keep (where noble ladies stay) you won't knock her up or so I thought.Clan tier has nothing to do with it. I’ve gotten wife pregnant before clan tier 2.
Try just leaving your wife in the town and then waiting (little + button to the right of town notables). I think it may get bugged sometimes when they are in your party.