Actually, it happened to me yesterday too. But I think I figured out what the problem is.
Maybe Tinkerer didn't realize something. WhenAlice reaches 20 days pregnant, it should automatically tell you that the baby has been born. I actually found this out through the Book of Girl.
Because the book told me Alice was 19 days pregnant. On day 20, it said she was no longer pregnant. And I... wait a minute, so what's happening now? And it happened that Alice was active both in the tavern and at the monastery at the same time.
The funny thing is, nothing breaks in the game. You just have to go to the tavern and finish Alice's quest, where she should then appear permanently at the monastery.
In fact, what I did was this: Alice in both the tavern and the monastery. I didn't talk to Alice at the monastery otherwise she told me that the baby was born and I had to give him a name. I went to the tavern, accepted the quest, told the father there's a monastery, and took Alice to the monastery. Afterwards, I spoke with her and named the newborn, since she had already given birth.
I think that Tinkerer should, in a sense block Alice pregnancy at 19* day, or with some girls who by mission are supposed to give birth to a baby only after finishing the mission connected to it.
In this case the related mission is the one where Alice's father wants to marry her off to a rich man. The MC will have to get her pregnant to keep her from marrying him. In my case, I had completely forgotten she was pregnant

and started doing other missions and other events... moral, I found myself with the mission of having to activate the lights of the monastery, and once the light was brought to the main ritual area, the girl was there, even though she shouldn't have been, since I hadn't yet finished the mission in which I discovered she was pregnant.