Sorry I just saw this now. Idk what part is bug or what part is intentional but if I used a male and female, but switched their positions, I could get the male pregnant. Sometimes when they were about to give birth that came up and not others,, and I couldn't figure out what the difference was. It was completely fine for a while then all of them had that prompt.
Also it seems if you have breed while one of them is pregnant, even if you go back on the save, the breeding shack is glitched into thinking every bottom is pregnant and you can no longer use it. It's corrupted more than one of my saves