I had that happen a few times too. I think it's just a little quirk of the game.

The "spare" baby usually disapears the moment you drag the mom somewhere, or when she begins a chore that involves picking up something, such as watering the crops, fishing, laundry, etc.

I like to think of it as she's like many real moms, and just doesn't want to "let go" of her baby, even when they've already left.