You gotta keep track of the family tree if you want to avoid this. I have been only setting a couple on breeding at a time so they can remain monogamous. Once they make a baby I take the male off breeding and put him back to whatever it was I had him doing before. I usually leave her on breeding for awhile and then if I have to leave and the game is going to remain going I'll set her to her specialty so she goes back to it after she's done caring for the little booger.