It seems like your objection is semantic, and depends on the meaning of "have." Does it mean, strictly, vaginal birth? Natural conception? Does a Cesarean section count? Does artificial fertilization count? Only if it's in-vitro?
It is stipulated that the babies are the direct genetic descendants of, and only of, the two female mice, and it appears that the babies are physically under (at least one of) their care. So the babies were produced by artificial assortative mating and are under the care of their their parents. If you think that artificial reproduction of any kind isn't really "having babies", where do you draw the line between what is or is not artificial?
I concede that "have babies" obviously has some generally agreed upon connotation beyond the literal meaning of the words; if I picked up someones’ babies at the park and said I "had babies," my statement would be regarded as unreasonable by almost everyone.
I'm not writing this just to be pedantic. I think artificial reproduction is interesting and sometimes controversial, because it invalidates our assumptions about reproduction.